diff --git a/Snakefile b/Snakefile
index 6b6bd58..e86c99f 100644
--- a/Snakefile
+++ b/Snakefile
@@ -10,17 +10,16 @@ Transcripts = config["polished_reads"]
rule all:
input:
- expand("/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_coding_potential_analysis.txt", gene = GENES),
- #expand("/home/annaldas/projects/result/{gene}/{gene}_blastx_protein_analysis.txt", gene = GENES)
- #expand("/home/annaldas/projects/result/{gene}/{gene}_sashimi.pdf", gene = GENES)
+ #expand("/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_transcripts_filtered_coding_potential_analysis.pdf", gene = GENES),
+ #expand("//project/owlmayerTemporary/Sid/isoform_analysis//result/{gene}/{gene}_blastx_protein_analysis.txt", gene = GENES)
+ expand("/project/owlmayerTemporary/Sid/isoform_analysis/result/all/{gene}_protein_sequences.txt", gene = GENES)
rule gene_transcript:
input:
NanoporeGTF,
Transcripts
output:
- "/home/annaldas/projects/result/{gene}/{gene}_seq.fa"#,
- #"/home/annaldas/projects/result/{gene}/{gene}_sashimi.sh"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_seq.fa"
params:
gene = "{gene}"
script:
@@ -28,10 +27,10 @@ rule gene_transcript:
rule blastx:
input:
- gene_fa = "/home/annaldas/projects/result/{gene}/{gene}_seq.fa",
+ gene_fa = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_seq.fa",
db = config["human_protein"]
output:
- "/home/annaldas/projects/result/{gene}/{gene}_blastx.out"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_blastx.out"
threads:
4
shell:
@@ -40,10 +39,10 @@ rule blastx:
rule protein_sequence:
input:
- blastx = "/home/annaldas/projects/result/{gene}/{gene}_blastx.out",
+ blastx = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_blastx.out",
db = config["human_protein"]
output:
- "/home/annaldas/projects/result/{gene}/{gene}_blastx_protein.fa"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_blastx_protein.fa"
shell:
"sh protein_transcript_sequences.sh {input.blastx} {input.db} {output}"
@@ -53,53 +52,70 @@ rule utr_regions:
params:
gene = "{gene}"
output:
- "/home/annaldas/projects/result/{gene}/{gene}_utr_regions.bed"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_utr_regions.bed"
script:
"utr_regions.py"
rule utr_sequences:
input:
hg = config["human_genome"],
- utr = "/home/annaldas/projects/result/{gene}/{gene}_utr_regions.bed"
+ utr = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_utr_regions.bed"
output:
- "/home/annaldas/projects/result/{gene}/{gene}_utr_regions.fa"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_utr_regions.fa"
shell:
"bedtools getfasta -fi {input.hg} -bed {input.utr} -fo {output} -name"
-rule transcript_filter_utr:
- input:
- utr = "/home/annaldas/projects/result/{gene}/{gene}_utr_regions.fa",
- seq = "/home/annaldas/projects/result/{gene}/{gene}_seq.fa"
- output:
- "/home/annaldas/projects/result/{gene}/{gene}_seq_filt.fa"
- script:
- "filter_utr.py"
+#rule transcript_filter_utr:
+# input:
+# utr = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_utr_regions.fa",
+# seq = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_seq.fa"
+# output:
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_seq_filt.fa"
+# script:
+# "filter_utr.py"
checkpoint mapping:
input:
- "/home/annaldas/projects/result/{gene}/{gene}_seq_filt.fa"
+ utr = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_utr_regions.fa",
+ seq = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_seq.fa"
output:
- directory("/home/annaldas/projects/result/{gene}/transcripts") #/{transcript}/{transcript}_map_protein.fa"
+ directory("/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts") #/{transcript}/{transcript}_map_protein.fa"
params:
gene = "{gene}"
script:
"translation_protein.py"
+def aggregate_mapping(wildcards):
+ checkpoint_output = checkpoints.mapping.get(**wildcards).output[0]
+ return expand("/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa",
+ gene=wildcards.gene,
+ transcript=glob_wildcards(os.path.join(checkpoint_output,"{transcript}_map_protein.fa")).transcript)
+
+rule aggregate_mapping:
+ input:
+ aggregate_mapping
+ output:
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/all/{gene}_protein_sequences.txt"
+ params:
+ gene = "{gene}"
+ shell:
+ "cat {input} > {output}"
+
rule iupred2a_analysis:
input:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa",
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa",
config["iupred2a"]
output:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_transcript_sequence.txt",
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_iupred2a.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_transcript_sequence.txt",
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein_iupred2a.txt"
script:
"iupred2a_analysis.py"
rule interpro_scan:
input:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa"
output:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map.gff3"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map.gff3"
params:
db = "Pfam,ProDom,Gene3D,CDD,Coils,MobiDBLite,SMART"
shell:
@@ -107,10 +123,10 @@ rule interpro_scan:
rule brewery_analysis:
input:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa"
output:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa.ss3"
- #"/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa.ss8"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa.ss3"
+ #"/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa.ss8"
params:
brewery = config["brewery"]
shell:
@@ -118,9 +134,9 @@ rule brewery_analysis:
rule functional_site_analysis:
input:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa"
output:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_sites.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein_sites.txt"
params:
ps_scan = config["prosite_scan"],
prosite_dat = config["prosite_dat"]
@@ -129,18 +145,18 @@ rule functional_site_analysis:
rule individual_transcript_analysis:
input:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_iupred2a.txt",
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map.gff3",
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa.ss3",
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_sites.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein_iupred2a.txt",
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map.gff3",
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein.fa.ss3",
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein_sites.txt"
output:
- "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_analysis.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein_analysis.txt"
script:
"transcript_analysis.py"
def aggregate_input(wildcards):
checkpoint_output = checkpoints.mapping.get(**wildcards).output[0]
- return expand("/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_analysis.txt",
+ return expand("/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}_map_protein_analysis.txt",
gene=wildcards.gene,
transcript=glob_wildcards(os.path.join(checkpoint_output,"{transcript}_map_protein.fa")).transcript)
@@ -148,7 +164,7 @@ rule aggregate:
input:
aggregate_input
output:
- "/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
params:
gene = "{gene}"
shell:
@@ -156,26 +172,28 @@ rule aggregate:
#rule filter_transcripts:
# input:
-# "/home/annaldas/projects/result/{gene}/{gene}_transcripts_analysis.txt"
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_transcripts_analysis.txt"
# output:
-# "/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
# script:
# "filter_transcripts.py"
rule protein_coding_potential_analysis:
input:
- "/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
output:
- "/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_coding_potential_analysis.txt"
+ "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_transcripts_filtered_coding_potential_analysis.pdf"
+ params:
+ gene = "{gene}"
script:
"interproscan_analysis.py"
#rule protein_domain_analysis:
# input:
-# "/home/annaldas/projects/result/{gene}/transcripts/{transcript}/{transcript}_map.gff3",
-# "/home/annaldas/projects/result/{gene}/transcripts/{transcript}/{transcript}_map_protein_iupred2a.txt"
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}/{transcript}_map.gff3",
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/transcripts/{transcript}/{transcript}_map_protein_iupred2a.txt"
# output:
-# "/home/annaldas/projects/result/{gene}/{gene}_map_protein_analysis.txt"
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_map_protein_analysis.txt"
# params:
# gene = "{gene}"
# script:
@@ -183,11 +201,11 @@ rule protein_coding_potential_analysis:
#rule sashimi_plot:
# input:
-# sashimi_sh = "/home/annaldas/projects/result/{gene}/{gene}_sashimi.sh",
+# sashimi_sh = "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_sashimi.sh",
# sashimi_py = config["sashimi"],
# bams = config["input_bams"],
# gtf = NanoporeGTF
# output:
-# "/home/annaldas/projects/result/{gene}/{gene}_sashimi.pdf"
+# "/project/owlmayerTemporary/Sid/isoform_analysis/result/{gene}/{gene}_sashimi.pdf"
# shell:
# "sh {input.sashimi_sh} {input.sashimi_py} {input.bams} {input.gtf} {output}"
\ No newline at end of file
diff --git a/gene_transcripts.py b/gene_transcripts.py
index ef2b0f8..27cbc00 100644
--- a/gene_transcripts.py
+++ b/gene_transcripts.py
@@ -18,8 +18,6 @@
# Mapping oID to transcript id
# Mapping transcript id to exons
-ABI2_info = []
-
gene_oID = dict()
oID_tID = dict()
gene_pos = dict()
@@ -57,7 +55,7 @@
# Extracting isoforms from related genes
output = []
-gene = snakemake.params[0].upper()
+gene = snakemake.params[0]
for oID in gene_oID[gene]:
tID = oID_tID[transcripts[oID].id]
transID = tID_pos[tID]
diff --git a/genes.tab b/genes.tab
index ba1c398..b8a6956 100644
--- a/genes.tab
+++ b/genes.tab
@@ -1,2 +1,68 @@
gene_symbol
-RPS24
\ No newline at end of file
+AC112178.1
+AL133395.1
+AL590617.2
+ANO7
+APOOL
+BAK1
+BCKDHB
+CADM2
+CHRNA1
+CUZD1
+DACT3
+DENND5B
+DLEU7
+EBF2
+EPB41L5
+ERBB2
+ERGIC3
+FAIM
+FAM78B
+GDF1
+GLS
+HAGHL
+HOMEZ
+IKBIP
+KCNH3
+KCNJ6
+KIF1B
+KIF7
+KLHL35
+KTN1-AS1
+LAGE3
+LARGE2
+LINC00467
+MIR302CHG
+MIR4787
+NCAN
+NECTIN2
+NKAIN3
+NKAIN4
+NRF1
+NRG1
+ONECUT2
+PDE4DIP
+PIWIL2
+PPP1R1C
+PRKCZ
+RAC3
+REEP1
+RENBP
+RGS9
+RIPOR2
+RPS24
+RRP7BP
+SGK3
+SLC17A7
+SLC44A3-AS1
+SLC6A15
+SNTG2
+SWSAP1
+SYNGR1
+THAP7-AS1
+THRA
+TLN1
+TPM2
+TYW1
+VSIG10
+WFDC2
\ No newline at end of file
diff --git a/interproscan_analysis.py b/interproscan_analysis.py
index 62037c5..0d639c6 100644
--- a/interproscan_analysis.py
+++ b/interproscan_analysis.py
@@ -1,11 +1,23 @@
+import argparse
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.patches import Rectangle
+from matplotlib.backends.backend_pdf import PdfPages
+
+
+
filename = snakemake.input[0]
file = open(filename, "r")
lines = file.readlines()
file.close()
+gene = snakemake.params[0]
+
class transcript:
- def __init__(self, tcons, idr, ips, ss8):
+ def __init__(self, tcons, length, idr, ips, ss8, pss):
self.tcons = tcons
+ self.length = length
self.idr = idr
self.ips = ips
self.ss8 = ss8
@@ -13,29 +25,29 @@ def __init__(self, tcons, idr, ips, ss8):
transcripts = dict()
+count = False
idr_lines = []
ips_lines = []
ss8_lines = []
-pss_lines = []
+pss_lines = dict()
for line in lines:
if (line.startswith(">")):
- if (len(ips_lines) > 0):
- transcripts[tcons] = transcript(tcons, idr, ips, ss8)
-
+ if (count):
+ if ((tcons not in transcripts) or ((len(idr_lines) - 1) > transcripts[tcons].length)):
+ transcripts[tcons] = transcript(tcons, len(idr_lines) - 1, idr_lines, ips_lines, ss8_lines, pss_lines)
+ count = True
new = True
idr_lines = []
ips_lines = []
ss8_lines = []
- pss_lines = []
+ pss_lines = dict()
idr = False
ips = False
ss8 = False
pss = False
- tcons = line[1:].strip().split("|")[0]
-
-
- if (line.startswith("#####IUPred2A Analysis")):
+ tcons = line[1:].strip().split("|")[0]
+ elif (line.startswith("#####IUPred2A Analysis")):
idr = True
elif (line.startswith("#####InterProScan")):
ips = True
@@ -43,17 +55,288 @@ def __init__(self, tcons, idr, ips, ss8):
elif (line.startswith("#####BrewerySS8 Analysis")):
ss8 = True
ips = False
-
- if (idr):
- idr_lines.append(line.strip())
+ elif (line.startswith("#####PrositeScan Analysis")):
+ pss = True
+ ss8 = False
+ elif (idr):
+ idr_lines.append(line.strip().split("\t"))
elif (ips):
- ips_lines.append(line.strip())
+ ips_lines.append(line.strip().split("\t"))
elif (ss8):
- ss8_lines.append(line.strip())
+ ss8_lines.append(line.strip().split("\t"))
+ elif (pss):
+ if (line.startswith("#")):
+ pss_id = line.strip().split(" ")[3]
+ pss_lines[pss_id] = []
+ else:
+ pss_lines[pss_id].append(line.strip().replace(" "," ").split(" "))
+
+if ((tcons not in transcripts) or ((len(idr_lines) - 1) > transcripts[tcons].length)):
+ transcripts[tcons] = transcript(tcons, len(idr_lines) - 1, idr_lines, ips_lines, ss8_lines, pss_lines)
+
+longest_length = 0
+longest_tcon = ""
+for ids in transcripts:
+ if (transcripts[ids].length > longest_length):
+ longest_length = transcripts[ids].length
+ longest_tcon = ids
+
+# PLOTTING
+
+colors=['#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231', '#911eb4', '#46f0f0',
+ '#f032e6', '#bcf60c', '#fabebe', '#008080', '#e6beff', '#9a6324', '#fffac8',
+ '#800000', '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080', '#ffffff']
+ss3_abbvs = ["H","E","C"]
+aa_abbvs = ["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y"]
+
+def preprocessArguments(args):
+ if args.geneNames != '':
+ gene_id='gene_name'
+ with open(args.geneNames,'r') as f:
+ targets=[i.strip() for i in f]
+ elif args.geneIDs != '':
+ gene_id='gene_id'
+ with open(args.geneIDs,'r') as f:
+ targets=[i.strip() for i in f]
+ annotation=pd.read_csv(args.gtf, delimiter='\t', header=None, usecols=[0,2,3,4,6,8],
+ names=['chrm','type','start','stop','strand','more'])
+ annotation['transcript_id']=annotation.apply(lambda x:
+ x['more'].split('transcript_id "')[1].split('"')[0],1)
+ annotation=annotation.drop(columns='more')
+ data=pd.read_csv(args.csv)
+ samples=data.columns[~(data.columns.str.startswith('feature')|data.columns.str.startswith('gene')|data.columns.str.startswith('transcript'))]
+ #conditions=list(set([x.split('_')[0] for x in samples]))
+ #conditions = ["0","3","5"]
+ conditions = ["day0","day3","day5"]
+ conditions.sort()
+ number_replicates={}
+ numerical=True
+ for cond in conditions:
+ number_replicates[cond]=samples.str.startswith(cond).sum()
+ try:
+ float(cond)
+ except:
+ numerical=False
+ x=np.arange(len(conditions))
+ if numerical:
+ x=[float(cond) for cond in conditions]
+ return gene_id, targets, annotation, data, samples, conditions, number_replicates, x
+
+def calculateStatistics(df,conds,nreps):
+ for cond in conds:
+ df['mean'+cond]=df.filter(like=cond+'_').mean(1)
+ df['stdn'+cond]=df.filter(like=cond+'_').std(1)/np.sqrt(nreps[cond])
+ df=df.sort_index()
+ return df
+
+def chooseIsoforms2Plot(df,minTPM,minPct,maxIso,annotation):
+ df['minimum']=df.filter(regex='^mean').min(axis=1)
+ df=df[df['minimum']>minTPM]
+ df['maximumPct']=df.filter(regex='^Pct').min(axis=1)
+ df=df[df['maximumPct']>minPct]
+ df['maximum']=df.filter(regex='^mean').max(axis=1)
+ df=df.sort_values('maximum',ascending=False)
+ df=df.head(maxIso)
+ return df
+
+def plotProfiles(x, df, df_gene, ax, colors, total=True):
+ if total:
+ plt.errorbar(x,df_gene.filter(like='mean').iloc[0],yerr=df_gene.filter(like='stdn').iloc[0],color='black',linewidth=2, label = "Total Expression")
+ for j in range(df.shape[0]):
+ row=df.iloc[j]
+ plt.errorbar(x+np.random.normal(0, 0.03, len(x)),row.filter(regex='^mean'),yerr=row.filter(like='stdn'),color=colors[j],linewidth=2, label = "")
+ ax.spines['top'].set_visible(False)
+ ax.spines['right'].set_visible(False)
+ ax.spines['left'].set_bounds(0,ax.get_yticks()[-2])
+ ax.spines['bottom'].set_bounds(min(x),max(x))
+ plt.xlabel("Day")
+ plt.ylabel("Normalized DeSeq2 TPM")
+ plt.legend(loc = "upper center", bbox_to_anchor=(0.5,1), frameon=False)
+
+def plotStacked(x,df,ax,colors):
+ plt.stackplot(x,df.filter(regex='^Pct').values,colors=colors[:df.shape[0]])
+ ax.spines['top'].set_visible(False)
+ ax.spines['right'].set_visible(False)
+ ax.spines['left'].set_bounds(0,100)
+ ax.spines['bottom'].set_bounds(min(x),max(x))
+ ax.axis([min(x),max(x),0,100])
+ plt.xlabel("Day")
+ plt.ylabel("TPM Percentage (out of 100%)")
+
+def prepareAnnotation(annotation,df):
+ cut=annotation[annotation['transcript_id'].isin(df['transcript_id'].values)]
+ strand=cut.iloc[0]['strand']
+ if strand=='+':
+ start=cut['start'].min()
+ cut['plot_start']=cut['start']-start
+ cut['plot_stop']=cut['stop']-start
+ else:
+ start=cut['stop'].max()
+ cut['plot_start']=(cut['start']-start)*(-1)
+ cut['plot_stop']=(cut['stop']-start)*(-1)
+ return cut
+
+def plotAnnotation(annotation, df, plt, colors, length):
+ transcripts_ids = []
+ transcripts_pos = []
+ chrm = ""
+ longest = annotation.loc[annotation['plot_stop'].idxmax()]["plot_stop"]
+ count = 3
+ panels = df_temp.shape[0] + 1
+ for j in range(df.shape[0]):
+ ax=plt.subplot(panels,2,(count,count+1))
+ ax.set_xlim((-50, length))
+ ax.set_ylim((-0.85, 1.85))
+
+ transcript_annotation=annotation[annotation['transcript_id']==df.iloc[j]["transcript_id"]]
+ transcripts_ids.append(df.iloc[j]["transcript_id"])
+ transcripts_pos.append(df.shape[0]-j)
+ if (transcript_annotation.shape[0] > 2):
+ for idx,row in transcript_annotation.iterrows():
+ chrm = row["chrm"]
+ if row['type']=='transcript':
+ plt.plot([row['plot_start']*length/longest,row['plot_stop']*length/longest],[1.75,1.75],color=colors[j],linewidth=2)
+ else:
+ plt.plot([row['plot_start']*length/longest,row['plot_stop']*length/longest],[1.75,1.75],color=colors[j],linewidth=10)
+ ax.spines['top'].set_visible(False)
+ ax.spines['right'].set_visible(False)
+ ax.spines['left'].set_visible(False)
+ ax.spines['bottom'].set_bounds(0,ax.get_xticks()[-2])
+ #plt.yticks(transcripts_pos,transcripts_ids)
+ #plt.xlabel(chrm)
+ count += 2
-transcripts[tcons] = transcript(tcons, idr, ips, ss8)
+def plotCodingPotential(plt, panels, df_temp):
+ count = 3
+ for ids in list(df_temp["transcript_id"]):
+ ax = plt.subplot(panels,2,(count,count+1))
+ flip = True
+ tcons_curr = transcripts[ids]
+ # Pfam domain
+ for i in tcons_curr.ips:
+
+ start = int(i[3])
+ stop = int(i[4])
+
+ if (i[1] == "Pfam"):
+ name = i[8].split(";")[3].split("=")[-1]
+ plt.gca().add_patch(Rectangle((start,1.05),stop-start,0.2,edgecolor="#3cb44b",facecolor='#3cb44b'))
+ if (flip):
+ ax.annotate(name,(start + (stop-start)/2.0,1.2), fontsize = 14, color = "#e6194b", ha = "center", va = "center")
+ else:
+ ax.annotate(name,(start + (stop-start)/2.0,1.1), fontsize = 14, color = "#e6194b", ha = "center", va = "center")
+ flip = not flip
+
+ ax.annotate("Pfam Domain",(-50,1.15), fontsize = 12, color = "#3cb44b", ha = "center", va = "center")
+
+ # Secondary structure prediction
+ ss8_df = pd.DataFrame(tcons_curr.ss8[1:], columns = tcons_curr.ss8[0])
+ ss = list(ss8_df["SS"])
+ for i in range(tcons_curr.length):
+ plt.gca().add_patch(Rectangle((i,-0.4),1,0.35,edgecolor=colors[ss3_abbvs.index(ss[i])],facecolor=colors[ss3_abbvs.index(ss[i])]))
+
+ plt.plot((0,longest_length),(1,1),color = "black")
+ plt.plot((0,longest_length),(0,0),color = "black")
+ plt.plot((-1,-1),(1.5,-0.9),color = "black")
+ ax.annotate("SS Prediction",(-50,-0.2), fontsize = 12, color = "#3cb44b", ha = "center", va = "center")
+
+ # Amino acid sequence
+ aa = list(ss8_df["AA"])
+ for i in range(tcons_curr.length):
+ plt.gca().add_patch(Rectangle((i,-0.8),1,0.35,edgecolor=colors[aa_abbvs.index(aa[i])],facecolor=colors[aa_abbvs.index(aa[i])]))
+ ax.annotate("AA Sequence",(-50,-0.6), fontsize = 12, color = "#3cb44b", ha = "center", va = "center")
+
+ #plt.plot((0,longest_length),(1,1),color = "black")
+ #plt.plot((0,longest_length),(0,0),color = "black")
+ #plt.plot((-1,-1),(1.5,-0.5),color = "black")
+
+ # IDR prediction
+ idr_df = pd.DataFrame(tcons_curr.idr[1:], columns = tcons_curr.idr[0])
+ idr_df = idr_df.astype({'# POS': 'int32',"IUPRED2":"float"})
+ plt.plot(idr_df["# POS"],idr_df["IUPRED2"])
+ ax.annotate("IDR Prediction",(-50,0.5), fontsize = 12, color = "#3cb44b", ha = "center", va = "center")
+
+ # Phosphorlyation Site
+ buffer = 0
+ for site_type in tcons_curr.pss:
+ for i in tcons_curr.pss[site_type]:
+ start = int(i[0])
+ stop = int(i[2])
+ plt.gca().add_patch(Rectangle((start,1.3+buffer),stop-start,0.025,edgecolor="black",facecolor='black'))
+ ax.annotate(site_type,(-50,1.3 + buffer), fontsize = 9, color = "#e6194b", ha = "center", va = "center")
+
+ #plt.gca().add_artist(plt.Circle((start + (stop - start)/2,1.35),0.25,color="black"))
+ buffer += 0.075
+
+ ax.spines['top'].set_visible(False)
+ ax.spines['right'].set_visible(False)
+ ax.set_yticks([], [])
+
+ ax.title.set_text(tcons_curr.tcons)
+
+ count += 2
+
+class Parser(object):
+ def __init__(self, csv, gtf, geneIDs, geneNames, outDir, minTPM, maxIso, minPct):
+ self.csv = csv
+ self.gtf = gtf
+ self.geneIDs = geneIDs
+ self.geneNames = geneNames
+ self.outDir = outDir
+ self.minTPM = minTPM
+ self.maxIso = maxIso
+ self.minPct = minPct
+
+args = Parser('/project/owlmayerTemporary/Sid/nanopore-analysis/Results_5_1/Quantification/all_counts_deseq2norm.txt',
+ '/project/owlmayerTemporary/Sid/nanopore-analysis/Results_5_1/GffCompare/nanopore.combined.gtf',
+ '', '/home/annaldas/projects/isoform_differentiation/test/list.txt',
+ '/home/annaldas/projects/isoform_differentiation/test/',0,18,0)
+
+outdir=args.outDir
+minimumTPM = args.minTPM
+minimumPct = args.minPct
+maximumIso = args.maxIso
+(identifier, targets, annotation, data, samples, conditions, number_replicates, x) = preprocessArguments(args)
+df=data[data[identifier]==gene]
+df_temp = df
+for j in range(df.shape[0]):
+ transcript_annotation=annotation[annotation['transcript_id']==df.iloc[j]["transcript_id"]]
+ if (transcript_annotation.shape[0] < 3):
+ df_temp = df_temp[df_temp["transcript_id"] != df.iloc[j]["transcript_id"]]
+# total gene expression calculation
+data_gene=df_temp[samples].sum().to_frame().transpose()
+data_gene=calculateStatistics(data_gene,conditions,number_replicates)
+# mean transcript expression calculation
+df_temp=calculateStatistics(df_temp,conditions,number_replicates)
+# isoform percentage calculation
+df_temp=(df_temp.filter(like='mean').div(data_gene.filter(like='mean').values[0],1)*100).add_prefix('Pct_').join(df_temp)
+#choose isoforms to plot
+df_temp=chooseIsoforms2Plot(df_temp,minimumTPM,minimumPct,maximumIso,annotation)
+x = [0,3,5]
+if df_temp.shape[0]:
+ panels = df_temp.shape[0] + 1
+ fig,axes = plt.subplots(panels,2,figsize = (18,24))
+ fig.subplots_adjust(top = 0.95)
+ fig.suptitle(gene,fontsize=16)
+
+ #plot isoform expression
+ axg=plt.subplot(panels,2,1)
+ plotProfiles(x, df_temp, data_gene, axg, colors)
+
+ #plot isoform expression percentage
+ axt=plt.subplot(panels,2,2)
+ plotStacked(x,df_temp,axt,colors)
+
+ #prepare annotation
+ annotation_cut=prepareAnnotation(annotation,df_temp)
+
+ #plot annotation
+ #axa=plt.subplot(panels,2,(3,4))
+ plotAnnotation(annotation_cut, df_temp, plt, colors,longest_length)
+
+ plotCodingPotential(plt,panels,df_temp)
-print(transcripts)
\ No newline at end of file
+fig.savefig(snakemake.output[0])
\ No newline at end of file
diff --git a/isoform_transcripts.ipynb b/isoform_transcripts.ipynb
index 0c4f65c..c0882b9 100644
--- a/isoform_transcripts.ipynb
+++ b/isoform_transcripts.ipynb
@@ -23,7 +23,7 @@
},
{
"cell_type": "code",
- "execution_count": 25,
+ "execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
@@ -34,7 +34,7 @@
},
{
"cell_type": "code",
- "execution_count": 24,
+ "execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
@@ -71,28 +71,28 @@
},
{
"cell_type": "code",
- "execution_count": 51,
+ "execution_count": 32,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
- "['4e6fca82-c640-4aac-be00-57223afed52e|41',\n",
- " '0807443e-5f7f-4b1b-b59f-b6a737ad89a9|16']"
+ "['6356d404-48e6-4c7a-8fbd-5f6e7f9b42bc|5',\n",
+ " 'a5e2697c-74a1-4ac9-a5b2-d974af83137d|4']"
]
},
- "execution_count": 51,
+ "execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "gene_oID[\"MLLT1\"]"
+ "gene_oID[\"KTN1-AS1\"]"
]
},
{
"cell_type": "code",
- "execution_count": 26,
+ "execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
@@ -109,7 +109,7 @@
},
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
@@ -153,28 +153,16 @@
},
{
"cell_type": "code",
- "execution_count": 27,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "ename": "KeyError",
- "evalue": "'142e462f-f586-42fc-97b9-b2e3bfa1fd0d'",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-27-ad5dd960a8c2>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0moID_tID\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"142e462f-f586-42fc-97b9-b2e3bfa1fd0d\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;31mKeyError\u001b[0m: '142e462f-f586-42fc-97b9-b2e3bfa1fd0d'"
- ]
- }
- ],
+ "outputs": [],
"source": [
"oID_tID[\"142e462f-f586-42fc-97b9-b2e3bfa1fd0d\"]"
]
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -186,7 +174,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -208,7 +196,7 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -234,36 +222,9 @@
},
{
"cell_type": "code",
- "execution_count": 35,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "92b2df50-a034-43a9-a75a-ad52cbccf075|6 AKAP8L\n",
- "78c3fe18-5c83-402c-8269-c07aedbd40a4|3 c1554cca-de07-418f-9818-eca090c80b38 TCONS_00030383\n",
- "9a2337b7-740a-4725-838a-8847f42a61bc|6 392ae6cc-c2f2-47a3-bb89-3fdf6caa6719 TCONS_00030384\n",
- "fd563dd9-374b-4439-a696-517bcfe44fad|3 79b8683e-5bbc-4bdd-a545-b464ff3564e3 TCONS_00030385\n",
- "e172e6af-1c34-43dd-bdb6-3656d795a229|3 4a88e4c4-0501-49dc-b89a-1990cdbaf23c TCONS_00030386\n",
- "fc150c74-c6c6-4e61-b4d5-d3639c0dee91|33 89d79286-527c-427b-bb19-83b110feb370 TCONS_00030387\n",
- "84a1fcd2-ec02-488e-b1e0-706944cb8fc5|3 9f9ce2f8-92d1-4a3c-90f7-68fcda8fb148 TCONS_00030388\n",
- "e0325806-c4fd-4d16-a8a3-3cd3ee13cdfc|6 388b7956-d60f-42cc-948c-f607b14cab9d TCONS_00030389\n",
- "b655aec1-864d-418b-b78a-f19b975b80fb|21 6be26262-4cff-4aca-8f54-9c7b3e5bdf22 TCONS_00030390\n",
- "bdc78543-c0d2-4ef3-b74e-e60e1c97e9d0|8 ab1a0ddb-1b97-47bc-b004-6c34f2f09b6a TCONS_00030392\n",
- "db5576fd-1921-46ce-a0d2-412728ab9db8|3 c62aeaa1-b7c1-47ad-b0a3-9815ad439460 TCONS_00032730\n",
- "3fe42f15-a4d1-49ae-a646-64d71a8c43e6|3 36436437-fd4b-4802-b9da-0f048cb4c048 TCONS_00032731\n",
- "287bdde2-eb53-4bbc-b96a-5b26773c3dd8|9 36436437-fd4b-4802-b9da-0f048cb4c048 TCONS_00032733\n",
- "5a5a062a-2f6c-46d2-aea4-a5e80bbab920|3 21c301c2-0b56-4ee7-8b6b-27f35c89cb08 TCONS_00032734\n",
- "6464d1df-7486-4008-a0bb-40d6227027a5|5 fb469fcf-d099-4192-a71a-d5c4c4ae37ba TCONS_00032735\n",
- "1a232563-721a-4f76-83af-18a01a9cf221|10 fb469fcf-d099-4192-a71a-d5c4c4ae37ba TCONS_00032736\n",
- "43396b69-e18d-4578-903b-782887dd7340|4 fb469fcf-d099-4192-a71a-d5c4c4ae37ba TCONS_00032737\n",
- "8004538e-da37-43d1-b8cc-2e8cffc77383|3 fb469fcf-d099-4192-a71a-d5c4c4ae37ba TCONS_00032738\n",
- "3debe6b9-8564-4b1f-a8a5-8d3587e3a789|3 fb469fcf-d099-4192-a71a-d5c4c4ae37ba TCONS_00032739\n",
- "7ccaec48-68b4-416b-b2b8-79d9e200e14b|11 fb469fcf-d099-4192-a71a-d5c4c4ae37ba TCONS_00032740\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"print(tID_oID[\"TCONS_00032753\"],oID_gene[tID_oID[\"TCONS_00032753\"]])\n",
"\n",
@@ -277,7 +238,7 @@
},
{
"cell_type": "code",
- "execution_count": 42,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -298,30 +259,11 @@
},
{
"cell_type": "code",
- "execution_count": 60,
+ "execution_count": null,
"metadata": {
"scrolled": true
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "ABI2\n",
- " OJ32 OJ33 OJ34 class_code gene_id \\\n",
- "31847 12.061978 19.252866 14.095533 = ENSG00000138443.16 \n",
- "22086 16.082637 13.730726 17.263069 j ENSG00000138443.16 \n",
- "79409 11.200408 5.671387 5.384810 = ENSG00000138443.16 \n",
- "64102 3.159089 2.387952 1.583768 = ENSG00000138443.16 \n",
- "\n",
- " gene_name ref_transcript transcript_id \n",
- "31847 ABI2 ENST00000261017.9 TCONS_00035868 \n",
- "22086 ABI2 ENST00000295851.10 TCONS_00035869 \n",
- "79409 ABI2 ENST00000261018.11 TCONS_00035870 \n",
- "64102 ABI2 ENST00000424558.5 TCONS_00035871 \n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"group = df_rep1.groupby([\"gene_name\"])\n",
"\n",
@@ -337,44 +279,11 @@
},
{
"cell_type": "code",
- "execution_count": 56,
+ "execution_count": null,
"metadata": {
"scrolled": true
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "FUS\n",
- " OJ40 OJ41 OJ42 class_code gene_id \\\n",
- "45283 14.890654 7.486137 11.079592 j ENSG00000089280.18 \n",
- "53160 17.810391 4.277792 8.897248 = ENSG00000089280.18 \n",
- "68181 131.388127 31.816081 114.992736 = ENSG00000089280.18 \n",
- "55151 93.431557 28.073012 56.405196 j ENSG00000089280.18 \n",
- "58630 61.606433 41.173751 59.426903 = ENSG00000089280.18 \n",
- "64460 13.722760 3.208344 5.707669 j ENSG00000089280.18 \n",
- "47855 6.131446 2.138896 6.043414 c ENSG00000089280.18 \n",
- "84426 14.014734 6.951413 14.101299 c ENSG00000089280.18 \n",
- "36211 16.058549 6.416689 8.393630 c ENSG00000089280.18 \n",
- "35581 0.875921 0.267362 1.175108 x ENSG00000089280.18 \n",
- "9268 0.000000 0.267362 0.671490 s ENSG00000089280.18 \n",
- "\n",
- " gene_name ref_transcript transcript_id \n",
- "45283 FUS ENST00000254108.11 TCONS_00022528 \n",
- "53160 FUS ENST00000566605.5 TCONS_00022529 \n",
- "68181 FUS ENST00000254108.11 TCONS_00022530 \n",
- "55151 FUS ENST00000254108.11 TCONS_00022531 \n",
- "58630 FUS ENST00000487509.6 TCONS_00022532 \n",
- "64460 FUS ENST00000254108.11 TCONS_00022533 \n",
- "47855 FUS ENST00000487045.6 TCONS_00022534 \n",
- "84426 FUS ENST00000487509.6 TCONS_00022535 \n",
- "36211 FUS ENST00000254108.11 TCONS_00022536 \n",
- "35581 FUS ENST00000254108.11 TCONS_00023974 \n",
- "9268 FUS ENST00000254108.11 TCONS_00023975 \n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"group = df_rep2.groupby([\"gene_name\"])\n",
"count = 0\n",
@@ -392,21 +301,9 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "ename": "NameError",
- "evalue": "name 'df' is not defined",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-3-c66790573a00>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mgroup\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdf\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgroupby\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m\"gene_name\"\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 2\u001b[0m \u001b[0mcount\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mgene\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mitem\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mgroup\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0;32mif\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgene\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"TLL3\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mgene\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
- "\u001b[0;31mNameError\u001b[0m: name 'df' is not defined"
- ]
- }
- ],
+ "outputs": [],
"source": [
"group = df.groupby([\"gene_name\"])\n",
"count = 0\n",
@@ -431,7 +328,7 @@
},
{
"cell_type": "code",
- "execution_count": 76,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -455,7 +352,7 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -467,7 +364,7 @@
},
{
"cell_type": "code",
- "execution_count": 5,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -483,20 +380,9 @@
},
{
"cell_type": "code",
- "execution_count": 302,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "['gene_id \"ENSG00000203667.10\"', ' transcript_id \"ENST00000391839.6\"', ' gene_type \"protein_coding\"', ' gene_name \"COX20\"', ' transcript_type \"lncRNA\"', ' transcript_name \"COX20-202\"', ' level 2', ' transcript_support_level \"1\"', ' hgnc_id \"HGNC:26970\"', ' havana_gene \"OTTHUMG00000040401.2\"', ' havana_transcript \"OTTHUMT00000097176.1\"', ''] transcript\n",
- "['gene_id \"ENSG00000203667.10\"', ' transcript_id \"ENST00000391839.6\"', ' gene_type \"protein_coding\"', ' gene_name \"COX20\"', ' transcript_type \"lncRNA\"', ' transcript_name \"COX20-202\"', ' exon_number 1', ' exon_id \"ENSE00001899074.1\"', ' level 2', ' transcript_support_level \"1\"', ' hgnc_id \"HGNC:26970\"', ' havana_gene \"OTTHUMG00000040401.2\"', ' havana_transcript \"OTTHUMT00000097176.1\"', ''] exon\n",
- "['gene_id \"ENSG00000203667.10\"', ' transcript_id \"ENST00000391839.6\"', ' gene_type \"protein_coding\"', ' gene_name \"COX20\"', ' transcript_type \"lncRNA\"', ' transcript_name \"COX20-202\"', ' exon_number 2', ' exon_id \"ENSE00003677820.1\"', ' level 2', ' transcript_support_level \"1\"', ' hgnc_id \"HGNC:26970\"', ' havana_gene \"OTTHUMG00000040401.2\"', ' havana_transcript \"OTTHUMT00000097176.1\"', ''] exon\n",
- "['gene_id \"ENSG00000203667.10\"', ' transcript_id \"ENST00000391839.6\"', ' gene_type \"protein_coding\"', ' gene_name \"COX20\"', ' transcript_type \"lncRNA\"', ' transcript_name \"COX20-202\"', ' exon_number 3', ' exon_id \"ENSE00001889952.1\"', ' level 2', ' transcript_support_level \"1\"', ' hgnc_id \"HGNC:26970\"', ' havana_gene \"OTTHUMG00000040401.2\"', ' havana_transcript \"OTTHUMT00000097176.1\"', ''] exon\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"info = list(pd_aline[\"info\"])\n",
"types = list(pd_aline[\"type\"])\n",
@@ -512,7 +398,7 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"metadata": {
"scrolled": true
},
@@ -523,28 +409,11 @@
},
{
"cell_type": "code",
- "execution_count": 15,
+ "execution_count": null,
"metadata": {
"scrolled": true
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "chr8\t26044860\t26045413\tENST00000520164\n",
- "chr8\t25841725\t25844611\tENST00000520164\n",
- "chr8\t26041288\t26041488\tENST00000408929\n",
- "chr8\t26040939\t26041002\tENST00000408929\n",
- "chr8\t26040616\t26040671\tENST00000408929\n",
- "chr8\t26040066\t26040101\tENST00000408929\n",
- "chr8\t25844362\t25844611\tENST00000408929\n",
- "chr8\t25858059\t25858083\tENST00000535548\n",
- "chr8\t25850594\t25850761\tENST00000535548\n",
- "chr8\t25844609\t25844640\tENST00000535548\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"df_utr_regions = pd.read_csv(\"/project/owlmayerTemporary/Sid/nanopore-analysis/ReferenceData/df_utr_regions.csv\")\n",
"\n",
@@ -567,7 +436,7 @@
},
{
"cell_type": "code",
- "execution_count": 32,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -589,19 +458,9 @@
},
{
"cell_type": "code",
- "execution_count": 33,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "1 TCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "392 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCATGTGTCTGGTTGTTTGAAA\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"if transcript_id in trans_utr:\n",
" seq = s\n",
@@ -614,43 +473,9 @@
},
{
"cell_type": "code",
- "execution_count": 30,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "-1 GGCATCGGCGCGGTCAGCCTCGTGGCGCGCCCACGCCCCCACGCCGGCTCTTCCCGGGGTCCTTCCGTGCGCGTTGATATGATTGGCCGGCGAATCGTGGTTCTCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "430 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCATGTGTCTGGTTGTTTG\n",
- "-1 GGCATCGGCGCGGTCAGCCTCGTGGCGCGCCCACGCCCCCACGCCGGCTCTTCCCGGGGTCCTTCCGTGCGCGTTGATATGATTGGCCGGCGAATCGTGGTTCTCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "-1 AAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCATGTGTCTGGTTGTTTGAAA\n",
- "-1 ATATGATTGGCCGGCGAATCGTGGTTCTCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "-1 GAAGTGTCTAGCAG\n",
- "430 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCATGTG\n",
- "1 TCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "-1 GAAGTGTCTAGCAG\n",
- "392 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTC\n",
- "1 TCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "392 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCA\n",
- "1 TCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "392 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCATGTGTCTGGTTGTTTGAAA\n",
- "1 TCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
- "-1 AATGTCACTGCCATGGCCGCCTTGCTGCATTTCTGAGGATGCTTCATCTCTCCACCTTCTTCTCCACTCAGCAGCCAGCAGGGCACTGTGGAAATCGGAGTCACATGAGCTGGCACCTCTGTTCAGAACCCTCCAGGGCTCCACATCTCTCTCACCCAAATGCCAAAGACCTCCCCACGCCCCCACAATCCCCCACGACCTGGCCACTGGCCTCCCACCACCTTCCAGCTCCAGCGGCTCCTACCACATTTAAGGCTTTCCTTCCTAGTTTTAATTTTTCCTCGTCAGCAGTTGATTTTATTATTTTCTTGTTTATTGGTATTTTCCCACTAGAAATGAAGCTGCGTGAAGTTAGAGATTTTTTTTTTTGGTCTGTGTTCCTAATTAGCTCATTGCTATACCCCTGGCGCCCAGAACAATGCCTTGGACACAGTACGCAGTAGACTAAATAAATACTTGTTGAATGACTGACTGACGGAATGACGGCTGTGTGGGGAGTGGATTGGGTCGTGAGGCAGAGGCTGCGGTGGAAACTCAGGCAGGAGGTGATGGTGGTTCTTGGGGCTGCGGAATGCCAAGTTTAGAAGCTCTTCCTCTGCTGTGGCACATGAACCGGTCACTCGAGAAGGCTTTTAGATTTACTTTGCCTAATCCCCTCTTAGTGCATGTGGGGAAACTGAGGTACACAAAAGGAATTCCCCACCAAGTTAGGGGCAGAACCTAGCCCCCTTGTCTCCCAGATGGATATCTTCTTTTTTTTTTGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTACCATCTTGGCTCACTGCAACCTCTGCTTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTGTCTGCGATTACAGGTGCACACAACCACGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTGGTCAGGGTGACCTCAAACTCCTGACCTCATGATCCACCCAGCTCAGCCTCCCAACGTGCTGGGATTACAGGCATGAGCCACCGTGCCTGGCTGGACATCTTGTTATTAAAGCTTCTTCTCTCTTTGTAGGGGAGGGGGAGATGCCTCTGGTGGAGAAGACCAGTGTGGCAGTGACTGTGTCTGTTAGTGAACCTGGTGGCTGGTTGAGGGTCTGTCGTGGTGACTGAGGACACATACAAAGTGCTTTTCTCAGTGGTCACCTTGGTGTTGGTGAATAAGGGTCAGAAGATGGCTCCTGTCCTAGGGCACTGCCAGTCGGTTTGGAAGCTGAAATGCCTGCTTAGCAGTTTGAGGAAACACAGACCTTGGAGGATCTTCTGGTTGCCTCTTCAAGAATTCATTCTATTCCCCTTCTGCTCCCCAAATTTGCTTTTCTTGGGGTGGGTCTTGGTTGGCCTAAGCCAAGAAAGTATGGCATCTACTCCTTCCATAGCAATAGCTCAGGAATAGGCAGTGACCCAGACCTGAACCAATCAGTGCATGGAATTACCCCTGGCCAAAGTGGTTGATTGAGGCTGGGTGCAAGCAGAGTTGTGAGAAGGCTCCCATTTGGTGGTTGGAGAGATCGCACTTGCTCCAGAGGTCATAATGTGCAGATCTGAGGCTTGGAACTGCTGCAGACATTTTGCTACCACAAGTGAAGCCACCCTGACGACACAGTTGACAATTTGGAGCAGGGCAGAGCTGAGAGAACAGCAGGGAAACAGCCAGAGTCTTGCTCAAGCCTCCCTGAAGTATCTATACCCCTGGACTCTAGTTATGGGGGCTAATAAATGTTATATACTGTTTAAGGTA\n",
- "15 GCTGTCTGAAGATAGATCGCCATC\n",
- "-1 AGATGACTTGCCCCAAGTCCTTCAGCTCATTCATGCTGGGGAAAGGAGTAAGCTTCAGGCGTCTTCCCCTGGAGTTCACGCCACCTCTGACAGCAAGTGAGCCGTTTGCTACTCAAGTGCTGTTTCTTGCTTTTTTAAG\n",
- "-1 TGAGGGAATTGGGGCTTGGAGTGCAAGCATTGGGAAGAATTTCCCAGGAAGAGAGATGCACAGATGTGAAGAACTCGAAGGCAAGAGAAAGCCGGGGGGTTGTGTGGCAGGTAGAAGTGCCAGGACCGTGGAGCGTGTGGACATG\n",
- "-1 GAAGTGTCTAGCAGGTACTGAGATT\n",
- "430 GAGCTGGAGATTGGATCACAG\n",
- "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCA\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"for t in trans_utr:\n",
" seq = s\n",
@@ -665,7 +490,7 @@
},
{
"cell_type": "code",
- "execution_count": 21,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -678,27 +503,18 @@
"\n",
"a = '''GCTCAGTCCTCCAGGCGTCGGTACTCAGCGGTGTTGGAACTTCGTTGCTTGCTTGCCTGTGCGCGCGTGCGCGGACATGGCCTCAAACGATTATACCCAACAAGCAACCCAAAGCTATGGGGCCTACCCCACCCAGCCCGGGCAGGGCTATTCCCAGCAGAGCAGTCAGCCCTACGGACAGCAGAGTTACAGTGGTTATAGCCAGTCCACGGACACTTCAGGCTATGGCCAGAGCAGCTATTCTTCTTATGGCCAGAGCCAGAACACAGGCTATGGAACTCAGTCAACTCCCCAGGGATATGGCTCGACTGGCGGCTATGGCAGTAGCCAGAGCTCCCAATCGTCTTACGGGCAGCAGTCCTCCTACCCTGGCTATGGCCAGCAGCCAGCTCCCAGCAGCACCTCGGGAAGTTACGGTAGCAGTTCTCAGAGCAGCAGCTATGGGCAGCCCCAGAGTGGGAGCTACAGCCAGCAGCCTAGCTATGGTGGACAGCAGCAAAGCTATGGACAGCAGCAAAGCTATAATCCCCCTCAGGGCTATGGACAGCAGAACCAGTACAACAGCAGCAGTGGTGGTGGAGGTGGAGGTGGAGGTGGAGGTAACTATGGCCAAGATCAATCCTCCATGAGTAGTGGTGGTGGCAGTGGTGGCGGTTATGGCAATCAAGACCAGAGTGGTGGAGGTGGCAGCGGTGGCTATGGACAGCAGGACCGTGGAGGCCGCGGCAGGGGTGGCAGTGGTGGCGGCGGCGGCGGCGGCGGTGGTGGTTACAACCGCAGCAGTGGTGGCTATGAACCCAGAGGTCGTGGAGGTGGCCGTGGAGGCAGAGGTGGCATGGGGTAGGTGTCTCATGAGCCAGGGAGTATCTTTGGTGGGGAGTGTGGAGGATTGCATGAATCTCCCTGAAGCCAGTCCCTAGTGCATGGTTTAGTATTCTTGTTGTCTAGGGATCTGTGAGGGCTTTGATTTGGGGGCAGTGACTTTCTTTTTACATCCCCATTTTATTTTTGTGAGAACTTGGGAGCCTGAACTCCCATCCATACCACTGAATAGAGATTTTGAGTAATGATACTTGTTTCCAAAAAAAAAGAAACCATACATAGATACGTATGGATTGGAGTCATTAATATCCTAGGCAAGAAACATGGAAGTGAAGACTTCTTTCTCTGCAAGGGAAACCGATGATCCCACTCCTGGGAAATAGTAGGGAAACTTGGTATGTGTATTCCCATGTGTCCTCTAGGGAGTTGGTAATGGTTAACCTGACTTCAGCTTCCAGGAATTGGCTACTCTTCCCGTTTTCTATAGTCATTTGAATCCACGAGCTTGATTTGCACTAATTTGACCGACATTGATTTTGTGTGTGACTTGGTTTATGGGGCCAGCTGACTGAAGTAAGCAGACCTTTTGGGCAAAAATATGCTTTGACAGTGGTCTCCCACCTATTTGTTCCACTGTCTGCCTTCCCCTGGTTACTTAAAATTCATCAGCTTGTCCAACTGGACCTTCTTTCCTTCCTGCTGAAGTTGATTTGAAGTAAAACCTTAGATTTGATGTTAAAACAGTTGTCAAATCTGTTGGTAAATAAGATTTGAAGGACCCTACTCTGTCTCCCTTGAAAAAGGGGAGGAATGTCAGTGTTACTGTTTTTGGAAAAAGTAGATTTTTAAACCGAGTTTGGAAATGGTAAGTATGCAGAGGTGGGTGGGGGCAATCTCAAAAACGTGCAAAAATGAGGAAAACAAAAATGAGGAAATGTGTGCGTGTGTTTAATGCAAAACTTTAAAAAGAAAAACAACTGTTATGTGACTGTTAACTTGCTCTGCATTTTATGTGCCACAGGTATGAAAGGTGACATTGCAAAATACTCCGCTCTTCTCGCAGTGTAGAAGGGGTGACCCCGGGGGTTGGGGGAGATCAAAAACAGCTCAGTAGTTAGGACAGAGCTTAGCTAAGTTTGTCTTGCTTTAAGGGGAAGTTGCCTTTGGTTTTGACTTTTTATGGAATGGGGTTGGGTCTGCTTGCTGCTTTCAAAGCAAAAACCACAAAAATGTGTTCAAGGCTACCCCAGCCTGGTGTGAAATGTCTTCTGGGTAAATTGGGGTAGGGTTTTTAAACCAACTACTTGGTTGTCAACCACTTGCGACAAGAGGAAAAAAAAACATCTGCTCCATCGGAAGAACGACCAAGGAAAATGGGTTATTTTTTTTCCAGAGGAAATAGATAACGTAACCTTTTAAAGCAAAATCTTTATAAACTGTGTCTGAGAAATTGCACACGTGTGTGTGACATGCTCAAAGGTCAGACAAGGGGTGGTCAGGAAGGGATGTATTTTAGTAGCCACTTGTATCTTTTTCCAAAAACACCTACCCATGTTTGGGGAATGTTAAACAAAATCAAAAAACAACCTTTTGTAGCCGTTGGAAGCTTCATGTCCTTTCTTCTAACTTGTCTTCTCCAGCGGAAGTGACCGTGGTGGCTTCAATAAATTTGGTGGTAAGTGAACAGAGTTTCCAAAATTCCCAACTCCCAGCAATGCTTTGTCTGATTGTTCATTTGCAGATGTCTTAGCGTGTTAATTTAAATGTCAAAGGTTTTGAGGTGTCCAGAACCACCTCCAGAAAGGGGTAGGGTAGAATGCCACCTGTTGCCTGGTGTGTGCTAACCTGGAGCAGGTAGGGGTAAGACTCAATAGTCATCTTTTACCAAATGGGTTTGCCCCAGGTTAATAAGAGGGGTCTAGTAGGCCTTGGACTGGGCCGTTGCCACACCTGGCACTTAGTGACCATCATCATGAGAAACTGGAGAGTGCGTGCTGGAACACGTGGTGCCATCTTGGCTTTAGGATCCTTTTGATCGTTGTGTCCAAGGCTTGTGTGTGTGTGAGTGTGTGGGAGACAACTCCGAATGTTTAATTCTGGAAGAGGGATGTAACATTGCCCTGAGGATGGTGAAGTTGGTATACATTTATAAAGTACGGAATGGTGTCAATGAATGCAATTCTATGTATATGGACTTAACTGAGATGGGCAAATAGAAACTAGCTCTGGGAAGGAACATGTGCACTACTTCAAGAAAGATTGGAAGCATGTGTGGCTCATGGGAAATAACCAGGTCTTAAACAGCACAAACTGAATTCGTGGACCAGGAAGGTCTTAAACAGCACAAACTGAATTCATGGAAAAATGACAAATTTGAGAAGTCTCCCAGTAAGCTGGAACTTTTCTGGTTTGGTTAACAAAAGGTTTCTTGATTTGTTTCAAGATTTAAAGCCAAAGGTGTGGGTTCATGACTTAGGTGTCATTGCGTGTGGGTACAATATTTATATATGGCGAATTCAGATAAACATTGGTCAAAGATGGTCTCTGGAAAAACAAAATAGAGGCTGCATTACGGAAATAAGATTTCTGGTCTGTTCCCTGGGACATGCTTAAAAAATACAATAGCTATTATGTATGGTTTTTATTTTCATGTGGTTTCGGGGAAACAACACGGTTTTAAGGATGGTTTCTAAAGATGAAATTAAAAATTGTTCCACAAGGGTTAAGTGTCTGGTGGTAAAGTTGGGAGAAACTGGATGGATGCACATCGCATGGCTGGTGGCGAGCCCATCTCTCTTCTCTCGGGTGAGAGAACCGGGCCAAGCTGAGTTGGTTTGTTCACTTTAATGGGTCTCCGTTTCCCCTGCCACCTGTGCTGAGGACATTTCCCAGCCTGAGCTGGGGGAGGCAGCATTTGCTGAAGTGTGGAGTTGTCTCTGTGGAGACTCAAGTTACAGATCTTAAGGGGCCTGCCTAGAATTTTCTCCTCTGGGCAGGCGACCCAGGAAAGGGTTTGGAGTGAGGCTGTGAGCACTTACTTGATATTTTACAAGTTTGGATTTGGTGTTAATTTTTTTCCTTGTCCGTTTTTTCCTGTTGACTAACGGCTCATCTTTTCCTTGTTTTTGTTTTTTTTTTGTTCTTTTTTTCCATGTCACTAAAGGCCCTCGGGACCAAGGATCACGTCATGACTCCGAACAGGATAATTCAGACAACAACACCATCTTTGTGCAAGGCCTGGGTGAGAATGTTACAATTGAGTCTGTGGCTGATTACTTCAAGCAGATTGGTATTATTAAGACAAACAAGAAAACGGGACAGCCCATGATTAATTTGTACACAGACAGGGAAACTGGCAAGCTGAAGGGAGAGGCAACGGTCTCTTTTGATGACCCACCTTCAGCTAAAGCAGCTATTGACTGGTTTGATGGTAAAGAATTCTCCGGAAATCCTATCAAGGTCTCATTTGCTACTCGCCGGGCAGACTTTAATCGGGGTGGTGGCAATGGTCGTGGAGGCCGAGGGCGAGGAGGACCCATGGGCCGTGGAGGCTATGGAGGTGGTGGCAGTGGTGGTGGTGGCCGAGGAGGATTTCCCAGTGGAGGTGGTGGCGGTGGAGGACAGCAGCGAGCTGGTGACTGGAAGTGTCCTAATCCCACCTGTGAGAATATGAACTTCTCTTGGAGGAATGAATGCAACCAGTGTAAGGCCCCTAAACCAGATGGCCCAGGAGGGGGACCAGGTGGCTCTCACATGGGGGGTAACTACGGGGATGATCGTCGTGGTGGCAGAGGAGGCTATGATCGAGGCGGCTACCGGGGCCGCGGCGGGGACCGTGGAGGCTTCCGAGGGGGCCGGGGTGGTGGGGACAGAGGTGGCTTTGGCCCTGGCAAGATGGATTCCAGGGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAATTAGCCTGGCTCCCCAGGTTCTGGAACAGCTTTTTGTCCTGTACCCAGTGTTACCCTCGTTATTTTGTAACCTTCCAATTCCTGATCACCCAAGGGTTTTTTTGTGTCGGACTATGTAATTGTAACTATACCTCTGGTTCCCATTAAAAGTGACCATTTTAGTTAAA'''\n",
"\n",
- "a = '''AGTGCGGAGCCTTAGGCGGAGCGAAGAGAACCGGTCGCGGCAATCCTAGCGCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCCGCATCCGCTGCGGGAGTCCGAGCCGGAACCACACCCAAGTAGCTGCCCTTTCCTCTTCTGTCATCTCACCGCCCCACCACAGACCGCGTTCCCCGAGGAAACCGGCCGCCCACGCCCGGAGCATCCTCCCCTGTTGAGCGGGCGCTGACGGACCCGGCGGCATGATGCGGCTGCGAGGCTCGGGGATGCTGCGGGACCTGCTCCTGCGGTCGCCCGCCGGCGTGAGCGCGACTCTGCGGCGGGCACAGCCCTTGGTCACCCTGTGCCGGCGTCCCCGAGGCGGGGGACGGCCGGCCGCGGGCCCGGCTGCCGCCGCGCGACTCCACCCGTGGTGGGGCGGGGGCGGCTGGCCGGCGGAGCCCCTCGCGCGGGGCCTGTCCAGCTCTCCTTCGGAGATCTTGCAGGAGCTGGGCAAGGGGAGCACGCATCCGCAGCCCGGGGTGTCGCCACCCGCTGCCCCGGCGGCGCCCGGCCCCAAGGACGGCCCCGGGGAGACGGACGCGTTTGGCAACAGCGAGGGCAAAGAGCTGGTGGCCTCAGGTGAAAATAAAATAAAACAGGGTCTGTTACCTAGCTTGGAAGATTTGCTGTTCTATACAATTGCTGAAGGACAAGAGAAAATACCTGTTCATAAATTTATTACAGCACTCAAATCTACAGGATTGCGAACGTCTGATCCCAGGTTGAAAGAGTGTATGGATATGTTAAGATTAACTCTTCAAACAACATCAGATGGTGTCATGCTAGACAAAGATCTTTTTAAAAAATGTGTTCAGAGCAACATTGTTTTGTTGACACAAGCATTTAGAAGAAAGTTTGTGATTCCTGACTTTATGTCTTTTACCTCACACATTGATGAGTTATATGAAAGTGCTAAAAAGCAGTCTGGAGGAAAGGTTGCAGATTATATTCCTCAACTGGCCAAATTCAGTCCCGATTTGTGGGGTGTGTCTGTTTGTACAGTAGATGGACAGAGGCATTCTACTGGAGATACCAAAGTTCCCTTCTGTCTTCAGTCCTGTGTAAAACCTTTGAAATATGCCATTGCTGTTAATGATCTTGGAACTGAATATGTGCATCGATATGTTGGAAAAGAGCCGAGTGGACTAAGATTCAACAAACTATTTTTGAATGAAGATGATAAACCACATAATCCTATGGTAAATGCTGGAGCAATTGTTGTGACTTCACTAATAAAGCAAGGAGTAAATAATGCTGAAAAATTTGACTATGTCATGCAGTTTTTGAATAAGATGGCTGGTAATGAATATGTTGGATTCAGTAATGCAACGTTTCAGTCTGAAAGAGAAAGTGGAGATCGAAATTTTGCAATAGGATATTACTTAAAAGAAAAGAAGTGTTTTCCAGAAGGCACAGACATGGTTGGTATATTAGACTTCTACTTCCAGCTGTGCTCCATTGAAGTGACTTGTGAATCAGCCAGTGTGATGGCTGCGACACTGGCTAATGGTGGTTTCTGCCCAATTACTGGTGAAAGAGTACTGAGCCCTGAAGCAGTTCGAAATACATTGAGTTTGATGCATTCCTGTGGCATGTATGACTTCTCAGGGCAGTTTGCTTTCCATGTTGGTCTTCCTGCAAAATCTGGAGTTGCTGGGGGCATTCTTTTAGTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTAAGGGAATTCACTTTTGTCACGATCTTGTTTCTCTGTGTAATTTCCATAACTATGATAATTTGAGACACTTTGCAAAAAAACTTGATCCTCGAAGAGAAGGTGGTGATCAAAGGGTAAAGTCAGTGATAAATCTTTTGTTTGCTGCATATACTGGAGATGTGTCTGCACTTCGAAGATTTGCTTTGTCAGCTATGGACATGGAACAGCGGGACTATGATTCTAGAACAGCACTCCATGTAGCTGCTGCAGAGGGTCATGTTGAAGTTGTTAAATTTTTGCTGGAAGCCTGCAAAGTAAACCCTTTCCCCAAGGACAGGTGGAATAACACTCCCATGGATGAAGCACTGCACTTTGGACACCATGATGTATTTAAAATTCTCCAAGAATACCAAGTCCAGTACACACCTCAAGGAGATTCTGACAACGGGAAGGAAAATCAAACCGTCCATAAGAATCTTGATGGATTGTTGTAATGGTCTCAAATCCCAAGATTTAAATCACTTACCTATTTAATTGTGGAAAATGATTATGAAGAACATGTGTATTTCTATCTGGTAGTGATGTATATTTTACATTTGTCATTTCAGTGTTACTGGAGTTTTCTTCATTGTGCACACAGGACAAATCTGATCTCTTTGGGAAAAAATAGAAATAAAACAATCTCCCTCCATAATGTGAGCAATATTACCTCGTGCATTGTATAATTTGATGTAAAAGAAATAGTTACCAATGCTAGCTTGTGTGGTCTTCCATGATTTATTTGTGTTTTGTGAATTTTCAATTTATGGTGATGATCTGCTGATATGCATTTATAAAGTAAGCTCTGTTGTACAGTCTGTCCAAATGGGTCAAGGTTGCCTTTAGAAGCAAATAGTGTGATTTTCAAGACTTCAAATACAAATTTAGTTTAAGTGTTTGAACAACTATATGCACTTACGGTTGTGTGTTTAAAATGTCTCTCTCACCCCCTAGCTTCATGATGTGACTCTTAAAAAACTATAATAGTTAACAACTGTTAGTAAGATAGACCAATTCTGATTAGACTTTATCAGGGAATCTGTTTAAGATATGTTTGGTGACCAAAACGTATGTGTGAATGTAGTTATAATGCTTTTGAAAAATTTTCCTTTTTCTATATCCCCTTAGTCCAGCCTCTCTTCTCAGACATTTAGCTATCTGCCTCTTTCCTTTAGCTGGGAAAGTGAGAGCTGGCATACTATGCAGTTTTTATGTTTTCCATAGTAAGTCAGAAAATGCCTCCTATTTCTGGCATCAGAACTTTGCCATTTGTCTACAGAAGACGAACCAGAGACAAAATTACTAAGTATAAATTAGTCAAGTTTATCAGTCTAAAAAACGAAGGGATGTGCAACTGCAGCTCTTTAAGAAGTTTTTTTTTTTTAGCTTCTAGGGTAAAGATAAATTCAGAAATGCTCTAAGCTACCAAAGTTATTCTGAAAGTATGGGAACTGCTACAACTAACAAACATTTGTTTCCAAGCCTGTCATTAAGAGTCTGCATCAAGAGATTTGTCCTCCTTGGGGGACCACTGGATCATTCCAGATTTCTTGTGATTTTTCTATTGTGTAATTCTTGGTGGGCTCTGTAGTTTAATAATAAGAAAAAGGCCATTTCATTTTAAATTGTGACCTATAATTCTTTGTCTTGGGTTGGTAATTCAGGATTCATTTGGAAAGTGGGTAAAAGGGGCTTCAAAAAACGGATAGAACAGGATTTTCTAGGAGTTACACATACATTTTATCCTGTCATACCTCGAGATAAAGTGGCATGTTAGTGAGGAGTTCTGATATTAAGCACACACACACATGCACACAAATGGACTTCTCTGAAGCTGTGTTTAGTGAAATGAGCTCAAGTACATGAATGTTAGTTGTTATCACATACAGCAAATTCCTTTTTTTTTCTTTTTCTATGAGCACACTCTGCTGCTTCTAAACTTTACATGCCTGATGGCACCTTACTCCAGCAGCCTCCAGGTGCTTTCATTTTCACTTCCAGTCTAAGCCAGTGGCTCCTGCCACTGCCCTCCCATTACCTAGATGGCACCTCCTTTGGTGAAACCACGGCCAATGTTCCTTAGCTGCACCAGGCCCGAAGCTGTTCCCATGCTTGAGCTTCCATGGGGAGGATGCTGAGTGAGCAGTTTCCTACCCCGTGGATCTAGCAAGCCATGGAGACAGGTAGCATTTGTAAGATGCTGCACAGGAGCAGCATTATCCCCAAAGATATTACAGGGTAGACACGTTTTAACTGAAATCAATCAAGATAACTTTATTCAAAGAGCAGCCCGCTTTGTGTGACTAAAATGAAACAAGACAGTTGAATTGTGTGACTTGAAGATTACCAATGATTTTGAGGCTTTTCTATAATAAAAAGAGGTTCTAACCATTATTTGGGAACAAAGAGAGTTTTCATCTTTTTTCAGATCAAAACCATTCTGTAAAATCTTTGTTGTTTAATTAAATGTGCCGTTATTTACCCCTGATGTTATTTATGACTATGTGCCGATTCCTGCTCGGGCTGTTTGCTGTTGGCTGGTAATAATATATTTGATTTAAATGCTGTTGACTGTGCTATTAACTGCTGCCGTCAGTAAACTCCAAAGATCTTTTTGTTTTGGCTTTAGTATCATATGTGCTTTTTCTGTATCCTGAGCGCTCTATATGATCATGTTAATTTAAAGCTTTATACACATTGTTGTTTTTGCTGGTCTCATCTTTGGTAATATGCTATACCCCACTGCTGCCCGACACTGCCCTTTAGCTGCAGAGCTGGATTAGCTGTTGACCATTTGATGCTGTTGTCTGTCTGGCAGGGACTGAATGACCTGATGTCAGATTTAGATTCTTCCTGGGGATTACACAGCTATGAATGTATTTGCTTCTAAAACCTCCCAAAGTGAATCTAATCTTAAAACTACAAGTTGTAAGTATTCTGAAATTGGGAAACATTTATTTTAAATGCAATCAGGTAGTGTTGCTTTTTACAGCATAATAAATATATGTATCAAAAAAAAAA'''"
+ "a = '''GGCTGCAGCCGGGCTCCGTGGCGCTCGCAGCCACCGCCTCCTCTCGGCTCCAGGTCTTCCCCTTCTTTTTACAACTGATCCTGTTGGGGATTTTTTTTTTTTCTAAATTGGAACGGTGGGGAGGAGCAGGGAGGGGGGACCTGGAGGAAGGGGAGAGATTAGGCAGCCATCAATTTCCTCCAGTTTCTCCCAGAACAGGTGATGCTTCTAAATTGTGATCACTTTCAGGAGGCAGCACTGCAGCTGGAAGGATGCGAGCGACCTAGGGTGGAGTGGCTGAGGCGGCAGATCTGAACTTGCGGAGGATAAGAACCCAAACTTTGACTACATCAGTCCGCACCTCGCCAGTGAAGCAAAGGACGGGTTATCTTTTTTTTTTTTCTAAGACTCAAACTTGGGCACTTGATCCCTTTTCTTGGATTGCTTTGGAGGAGACGATTTGCTGGCAACGTTGGGAACAGTCAGGACTGTGTTGTAACTCTTACTTTTAAAGCGACAGTAGAGGATCAGACTTTTTAAATGTTTGGAATTCAAGATACTTTAGGAAGAGGACCAACTCTGAAAGAGAAATCGCTGGGCGCGGAGATGGATTCGGTCAGGTCCTGGGTCCGGAATGTCGGAGTGGTGGACGCTAATGTCGCCGCGCAGAGCGGGGTCGCCCTGTCCCGGGCCCACTTTGAGAAACAGCCTCCTTCCAACTTGAGGAAATCCAACTTCTTTCACTTCGTCCTGGCGCTCTATGACAGGCAGGGCCAGCCGGTGGAGATCGAGCGGACGGCCTTCGTGGACTTTGTGGAGAATGACAAAGAACAAGGCAACGAGAAGACCAACAACGGCACTCACTACAAGTTACAGCTCCTCTACAGCAACGGTGTCCGCACGGAACAGGACCTCTATGTCAGGCTCATCGACTCGGTCACCAAGCAGCCCATCGCTTACGAGGGACAGAATAAGAATCCGGAAATGTGCCGAGTTCTCCTGACGCACGAAGTGATGTGTAGTCGATGCTGCGAAAAGAAAAGCTGTGGAAACCGAAATGAGACTCCATCGGACCCAGTCATAATTGACAGATTCTTTTTAAAATTTTTCCTCAAGTGCAATCAGAATTGTTTGAAAACAGCAGGAAACCCAAGGGACATGAGACGGTTTCAGGTTGTGTTGTCAACAACGGTGAATGTGGATGGACACGTCCTGGCTGTTTCTGACAACATGTTTGTTCATAACAACTCCAAGCATGGACGGAGAGCAAGAAGACTCGATCCATCGGAAGCTACCCCCTGCATCAAAGCCATTAGCCCGAGTGAAGGCTGGACCACAGGAGGAGCCATGGTCATCATCATCGGGGACAACTTCTTTGATGGTCTCCAAGTGGTGTTTGGGACTATGCTTGTATGGAGCGAGCTAATAACCCCTCATGCCATCAGAGTACAGACTCCTCCCCGGCACATCCCAGGCGTGGTAGAGGTGACATTATCTTATAAATCTAAACAGTTCTGCAAAGGAGCCCCAGGAAGGTTCATTTACACAGCATTAAATGAACCCACCATAGACTATGGCTTCCAGAGACTGCAGAAGGTCATCCCTAGGCATCCTGGAGATCCTGAGAGATTAGCTAAGGAGATGCTGTTGAAAAGAGCTGCAGATCTAGTGGAAGCTCTTTATGGCACACCACACAATAACCAGGACATCATTTTGAAGCGAGCCGCAGACATTGCTGAAGCTCTCTACAGCGTCCCCAGGAATCCCAGCCAGCTTCCAGCCCTCTCTAGCTCCCCAGCGCACAGTGGCATGATGGGAATCAACTCCTATGGCAGCCAGCTTGGGGTCAGCATCTCAGAGTCAACACAAGGAAATAATCAAGGGTACATCCGCAACACAAGCAGCATCTCTCCGCGGGGATACTCTTCCAGCTCCACGCCTCAACAGTCTAATTACAGTACCTCCAGCAACAGTATGAATGGCTACAGCAATGTCCCCATGGCCAACTTGGGTGTTCCAGGTTCACCAGGATTTCTAAATGGCTCACCCACCGGCTCTCCTTATGGAATCATGTCATCAAGTCCCACCGTTGGGTCTTCCAGCACATCCTCCATCCTCCCATTTTCCTCTTCAGTTTTTCCTGCTGTCAAACAGAAGAGTGCCTTTGCCCCTGTCATCAGGCCCCAAGGCTCCCCTTCACCTGCCTGCTCCAGCGGCAATGGAAATGGATTCAGAGCCATGACCGGACTTGTTGTACCCCCGATGTAAAGAAGAACTGCTTTCTTATAGCACAAAACTACTTACTCTGATGGACCAATAATGAAGAAAGCACTAGGAGCTCTTTTGGGGGTGTAGTGGTGCCCCCACATGAACATGATGGACACCCTTGGGTCTGCAAGGAGCCAGCATCTTACTTGGTCCCACGTCCTCCTATAGCTCTGATGGTGGCTACACAAACTGACCCTCTTGGGACAAGGACAAAAGATGTCATTGACGTAGTCAGTGCTAAGAGCAGAAATGCAATTCTTTGTTATGAACATTATGAAAACCACCTTCCTATGTTTGTAAAATATTTAAGAAAAAATTGGCAAACAATTAATGCTTAATATTTTGGATACTATTTGTTTTTCTTTGTAGGAAAAAAAAGTTGAAAGTTTCTATTTTCTATGAAGCCTTTCAGATACCAATTTAGTTTATGCAGAAAAAAATTGAACAAAACAGGGTACCAGCACGGAAGACTTTCTTAAAACGCAACCTGAATTGAATGATGAAATGTTGTATGTGTGTTTGCTTATAGCTTAATCTCTTTAAAAAATGAACAAAAAAAA'''"
]
},
{
"cell_type": "code",
- "execution_count": 22,
+ "execution_count": null,
"metadata": {
"scrolled": true
},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "M+ANLGVPGSPGFLNGSPTGSPYGIM+SSSPTVGSSSTSSILPFSSSVFPAVKQKSAFAPVIRPQGSPSPACSSGNGNGFRAM+TGLVVPPM+_RRTAFL_HKTTYSDGPIM+KKALGALLGV_WCPHM+NM+M+DTLGSARSQHLTWSHVLL_L_WWLHKLTLLGQGQKM+SLT_SVLRAEM+QFFVM+NIM+KTTFLCL_NI_EKIGKQLM+LNILDTICFSL_EKKVESFYFL_SLSDTNLVYAEKN_TKQGTSTEDFLKTQPELNDEM+LYVCLLIA_SL_KM+NKKREKF_NVLQLFK_INV_LIVSRGRN_DLFLEERGISLPDVK_K_CKHVVTSFKGV_LLLQLLTRFLSPVLHPLLFHHFIDPRARTCRFPQNTLM+QKQTL_HM+HKYSNPSIHSQLRLISK_STLL_ILFKIPIISFQRSPLSSPENSHV_VCLRLSASQGKKHLTF_QSQNHRLS_PRDPLGIPPHQNPTTPSALGAWFSTEVHSPIELQQHGLEKITLFDGLFRVSLRTSKSFPLPVNFPFYGIKLS_KT_LCHSTVSSQE_DGM+WERDIKSPNPLF_CSKKGKTRFLGDPEIRGICVLCSTVTQPFDGLFIVL_LALRGEEPCLSC_QWLILESLCNPRDISRHIGIANKDVTCFHVGVLLIDS_APQ_SLYTDLVWGSWLGFQH_K_M+QHSWKNIM+SASEPILDDFINSAYLLFDPLM+QAHIYPAPTVLFAFNPFWNYPV_LILFLCT_ESKVLETWHAYNYC_QSLIVRA_SAKIHGNIREKVPQ_ET_LM+EGEECVEYECYLPKVKAEQN_ACLALDLSQSNIRKFCFF_VALLLEPVNFPFA_R_VQYCLQNDCRISW_LYTEKCV_LNTRHLDHSARTLAATELFNCTNVCKDYF_CTNKLKTKLPCPR_SLLFNHSSPKLFLCHLEYEYFYW_LQTLSCVCKRSCVRFFSFKGTIYFIIYLSFVIAL_FFSVFLCTFQYAWFKNH_LLYLLYSKVSFSHCIVSFYCFALSVIYSIKLLCTELFVKTAFLFTVFNGLT_RISCL_NEYVYFSFKL_IILTKK_NFCTVK\n",
- "WPTWVFQVHQDF_M+AHPPALLM+ESCHQVPPLGLPAHPPSSHFPLQFFLLSNRRVPLPLSSGPKAPLHLPAPAAM+EM+DSEP_PDLLYPRCKEELLSYSTKLLTLM+DQ__RKH_ELFWGCSGAPT_T_WTPLGLQGASILLGPTSSYSSDGGYTN_PSWDKDKRCH_RSQC_EQKCNSLL_TL_KPPSYVCKIFKKKLANN_CLIFWILFVFLCRKKKLKVSIFYEAFQIPI_FM+QKKIEQNRVPARKTFLKRNLN_M+M+KCCM+CVCL_LNLFKK_TKKGKNFKM+FYNYLNK_M+CNLL_VEVEIKTFFWKREGFLFLM+_NENDANM+__QVLKVCDYYCSYLLDSYPLSCTPSFSITLLTQGQEHVDSHRTP_CRNRHSSTCTNTPTHQFIPSSV_FLNSPHSCEYFLKFLLLAFNVLP_AVQRIPM+FESVSGFQHPKERSTSPSSRAKTTDFLNQGTPWEFLLTRTPPLPPLWVPGSVQRYTAP_NFSNTVWRR_LCLM+DSLESVLEHPSPFLSLSISPFM+ALNSLEKHSYATRQFLVKNETECGRGILKALIPSSDVRRKARPDSWEIQRLGASAFYAAQLPSPLM+GSSSFCD_LLEGKNLALAANSG_FLKAYVILETYPGILGLPIKM+SLVSTLGFSLLTHEHHNRVYTQT_FGVLGWDFSIRNRCSTHGKTS_VHLSQF_M+ISLILHTFSLTH_CRPTSIQPQLSYLPLTHSGITQYDLYYFYAHENPRF_KPGM+LITTADSPS_SGLKAPKYTET_EKKSPSEKPD_WKGKNVWNM+NVTFQK_RQSKIKHV_PWI_ANPT_GNFVFFK_HCF_NL_IFLLHEDECSTVFKM+IVEFLGSFTPKNACN_IPDILTIQLEPWQQQSYLIVQM+CVRIIFSVLIN_KQSYPVLVSHCYSIIPVPSYFCATWNM+SISIGNYKLYPVFVRGAV_DFFHLKGQFTSLFIFLLL_RCNSSQFFFAHFNM+HGLKTINFSTFCTVRFHFHTV_FHFIVLLCQLYTV_SCYAQSFL_RQLFCLLFLM+VLLKEYLVCKM+NM+STSVLNFKLS_QKNKIFVL_K\n",
- "GQLGCSRFTRISKWLTHRLSLWNHVIKSHRWVFQHILHPPIFLFSFSCCQTEECLCPCHQAPRLPFTCLLQRQWKWIQSHDRTCCTPDVKKNCFLIAQNYLL_WTNNEESTRSSFGGVVVPPHEHDGHPWVCKEPASYLVPRPPIALM+VATQTDPLGTRTKDVIDVVSAKSRNAILCYEHYENHLPM+FVKYLRKNWQTINA_YFGYYLFFFVGKKS_KFLFSM+KPFRYQFSLCRKKLNKTGYQHGRLS_NAT_IE__NVVCVFAYSLISLKNEQKKGKILKCFTII_INKCVTYCK_R_KLRPFFGRERDFSS_CKM+KM+M+QTCSNKF_RCVIITAVTY_ILIPCPAPPPFPSLY_PKGKNM+_IPTEHPNAETDTLAHAQILQPINSFPAPSDF_IVHTLVNTF_NSYY_LSTFSPEQSREFPCLSLSQAFSIPRKEAPHLLAEPKPQTFLTKGPLGNSSSPEPHHSLRFGCLVQYRGTQPHRTSATRFGEDNSV_WTL_SQS_NIQVLSSPCQFPLLWH_TLLKNIAM+PLDSF_SRM+RRNVGEGY_KP_SPLLM+FEERQDQILGRSRD_GHLRSM+QHSYPAL_WALHRFVTSS_RGRTLP_LLTVVDS_KLM+_S_RHIQAYWDCQ_RCHLFPRWGSPY_LM+STTIESIHRLSLGFLVGISALEIDAALM+EKHHECI_ANFR_FH_FCIPSL_PIDAGPHLSSPNCLICL_PILELPSM+TYIISM+HM+RIQGFRNLACL_LLLTVPHSQGLKRQNTRKHKRKSPPVRNLIDGRGRM+CGI_M+LPSKSEGRAKLSM+FSPGFEPIQHKEILFFLSSIAFRTCEFSFCM+KM+SAVLSSK_L_NFLVALHRKM+RVTKYQTS_PFS_NPGSNRAI_LYKCV_GLFLVY__IKNKATLSSLVIAIQSFQSQVIFVPLGI_VFLLVTTNSILCL_EELCKIFFI_RDNLLHYLSFFCYSVVILLSFSLHISICM+V_KPLTSLPFVQ_GFIFTLYSFILLFCFVSYIQYKVAM+HRAFCKDSFFVYCF_WSYLKNILFVK_ICLLQF_TLNYPNKKIKFLYCKK\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
+ "a = \"TGGACAGCTCCCGCTCACCCAAACAGAAGACGTCGGCGCCGGAGCGGGCTCGGACATGGCGAGGCTGCGAGCCGGCCCGAGCGGCGGGGCCCGGTGATCCCTCCCTCCCTCCCCGTCCCCTCCCCTCTCCCGCACGCACGCCCCGTCCGCCCCCACCCCGCCCCCACCCCGGGCGAGCCCGCCCGCAGCCCGGGGCGCACACCCGCACGCGCACTCCTCTCCACTCACTCCCGCGCCCGCCCCCACTCCCGCAGCCGAGCCCCGCCACGCGCGCCTTGCCCGCCCGCCGGCCGCCCCCGCCGCCCCCGCCGCCCCCGGGCCCTGATGGACTGAATGAAGGCTGCCTACACCGCCTATCGATGCCTCACCAAAGACCTAGAAGGCTGCGCCATGAACCCGGAGCTGACAATGGAAAGTCTGGGCACTTTGCACGGGCCGGCCGGCGGCGGCAGTGGCGGGGGCGGCGGCGGGGGCGGCGGGGGCGGCGGCGGGGGCCCGGGCCATGAGCAGGAGCTGCTGGCCAGCCCCAGCCCCCACCACGCGGGCCGCGGCGCCGCTGGCTCGCTGCGGGGCCCTCCGCCGCCTCCAACCGCGCACCAGGAGCTGGGCACGGCGGCAGCGGCGGCAGCGGCGGCGTCGCGCTCGGCCATGGTCACCAGCATGGCCTCGATCCTGGACGGCGGCGACTACCGGCCCGAGCTCTCCATCCCGCTGCACCACGCCATGAGCATGTCCTGCGACTCGTCTCCGCCTGGCATGGGCATGAGCAACACCTACACCACGCTGACACCGCTCCAGCCGCTGCCACCCATCTCCACCGTGTCTGACAAGTTCCACCACCCTCACCCGCACCACCATCCGCACCACCACCACCACCACCACCACCAGCGCCTGTCCGGCAACGTCAGCGGCAGCTTCACCCTCATGCGCGACGAGCGCGGGCTCCCGGCCATGAACAACCTCTACAGTCCCTACAAGGAGATGCCCGGCATGAGCCAGAGCCTGTCCCCGCTGGCCGCCACGCCGCTGGGCAACGGGCTAGGCGGCCTCCACAACGCGCAGCAGAGTCTGCCCAACTACGGTCCGCCGGGCCACGACAAAATGCTCAGCCCCAACTTCGACGCGCACCACACTGCCATGCTGACCCGCGGTGAGCAACACCTGTCCCGCGGCCTGGGCACCCCACCTGCGGCCATGATGTCGCACCTGAACGGCCTGCACCACCCGGGCCACACTCAGTCTCACGGGCCGGTGCTGGCACCCAGTCGCGAGCGGCCACCCTCGTCCTCATCGGGCTCGCAGGTGGCCACGTCGGGCCAGCTGGAAGAAATCAACACCAAAGAGGTGGCCCAGCGCATCACAGCGGAGCTGAAGCGCTACAGTATCCCCCAGGCGATCTTTGCGCAGAGGGTGCTGTGCCGGTCTCAGGGGACTCTCTCCGACCTGCTCCGGAATCCAAAACCGTGGAGTAAACTCAAATCTGGCAGGGAGACCTTCCGCAGGATGTGGAAGTGGCTTCAGGAGCCCGAGTTCCAGCGCATGTCCGCCTTACGCCTGGCAGCGTGCAAACGCAAAGAGCAAGAACCAAACAAAGACAGGAACAATTCCCAGAAGAAGTCCCGCCTGGTGTTCACTGACCTCCAACGCCGAACACTCTTCGCCATCTTCAAGGAGAACAAACGCCCGTCAAAGGAGATGCAGATCACCATTTCCCAGCAGCTGGGCCTGGAGCTCACAACCGTCAGCAACTTCTTCATGAACGCCCGGCGCCGCAGCCTGGAGAAGTGGCAAGACGATCTGAGCACAGGGGGCTCCTCGTCCACCTCCAGCACGTGTACCAAAGCATGATGGAAGGACTCTCACTTGGGCACAAGTCACCTCCAAATGAGGACAACAGATACCAAAAGAAAACAAAGGAAAAAGACACCGGATTCCTAGCTGGGGCCCTTCACTGGTGATTTGAAAGCACAATTCTCTTGCAAAGAAACTTATATTCTAGCTGTAATCATAGGCCAGGTGTTCTTCTTTTGTTTTTAATGGCTATGGAGTCCAAGTGCAAGCTGAAAAATTAATCTCTTAGAACCAGACACTGTTCTCTGAGCATGCTAAGCATCCCAGAAACCCAAATGGGGCCTTCCTGGAGCGAGTTAATTCCAGTATGGTGTCAACCAAGCTCGGGATTGCTTAAAATATCATCCATCCCACTTCAGGTCCTGTCAGCTTCTTGCAGTCAGAGTTCCTATGAGTAACAATAGGAGTTTGGCCTATGTAAGGACTCTGAGTTTAGGCTTCCAAGATACAACAATAAGAGAAGAATCTAGCAACGAGAATGACCTCATTTGCTTTCCACATGCTTAGCCTCATTATACCATGTTATGTCCAAGTTCACAGCCACAACATCAGAATGGTAATTACTGAGCACAAGTTTTAAATATGGACGTTAAAAAAAAAAATCCAAGGACCTGTTTTTCCAACCCAGACATCTTTTCATTGAATGATTTAGAAAGCTTTAAGTTGATCCAGCTTACAATTTTTTTTTTCTTTACCTCCTGGAAATCTCATATGGTCTTGGATCCGTCAAAAAAACCAGTCAGTTCACTTGCGCTCAAAGTATCAAGCACAACAAAGATAAACAGAAGTGAGGAAGGTTCTGGGTTCACTACATCTGGATTTTCAAGACACCTATTGTGAAGTCATTAGGGAATTGATGAGAATATGGCTTCAAGCACATTTTGCAGTTTGCTACAAATTCTGTTGTACATAATGCAGACGCACACTCAGGAGGCCAATTTAACTGTTAACAGTGCATGGAGCGAATGCAGCATTTTAAAAGATCTAGGTTTTTTTAGGTCATTAATGTGTCCTTGGTTGATCAGTCATCTGGTCCCTCCTACTGTGTGTTATGACCACCACGTAATCCATTCTCGCTCTTTCTGATTTGGGGTTTTTCCTCATCCATCCCATTAGTAGGGATGTTTTCTGTGTTTTCTAGCAAGAAAAAAAAATCAATCAATCAAACCTGCATACATGTTACTCATGACTGTCATCTAGTCCTAAATCTCTTCTGTTGTTGAATCATCCTTGCAAAACAGCTGAATACATCTGGAGAAAACACAGCACACCAAAGAAGCAGAATACTGCAAACCAAAGACATTTATGACTTGTCATTTTCTAGCCTAAAAATACTGTGATTACTTTTAGAAATCAGAAAACCTCTGCAACTCCGAATGGCATTCAGCTCTTGCATTTGGCGCATCATCGGGCTGAGCGGACCAGCTACACCAAGGACATTAGCCAAGCCACCCAGAGGGGTGGCTTTGCCACACCAGTTGTCACCTTCCCATAGCAAGTGGAAGAGCGCCCACAGAACTCTGGGAGATTGCAAAGGTCACAATGTGCATATTTACCAGTGAATGGCCCCGGGTGGGGCCACGTGGGGGTGTTCAAAGCAAGCCAAACGCTGCAATCATTCTTTACAGACACTTGAGACTGACTTTTTTATGAATTACTTAGTCGAAACCAAAGAAACTTTTTCTGCACCTACTTCTGCAACAAACAAAACTGTCCCATTAAAATGAATAAATAAATCCGTAAATCAATGGAAATCACCACCAATAAGAAGGAAGCACGCCAGAAAATAAACGAAAACAAAAACAGGGAGACACACTGTGTTCAAACAGACCTCTTGGGACATTTTTTGGAAGCAGATTTTAAAGAAAGGGTTGAGACAAAGATAGAAATAAGGAAGAGCCTCAGTGGCTGCTGCTTCATTTGACAACTCACACGGTAATCTTAAAGCTGAAGATTGTCTTTAATTTGTGCCTATGCAGTTTTTCAAAAGAACACGGAACAGAGCAACAGAAACCTCAACAGCTACAATACCAAAGATGAGGATTTCTCACACCTTTTGTTTCAGTTCATTATCTCCTCTTGCCTGGCTAAAATACTAATAGCGCCATTGAACTGTATAAAGGTAATCAATTATGTTTCTCTGAGCAACAAAAGGAAAGGGCCATTTATTTGATTTTATTGTTTCATTTCAATTTTGTCTTATGGTTTTTTGCCCCAACATGGAATCTCTCAAAAGTTTCCATGGACTCCAAGTTTAAGATGTTGGGATATTGAACAGTTCTCTCTGCTCAGCAGAGGGTAGGGAATAACATTATCACTTGAATGTTCTTTGCTTAACCCTTAGACTTGGTTCCTTCTATGTTCAGAGTCTCATCATCAGGGGAAGGAAAGGGAGTGAGGGTCAGGGATAGGGGTCTTGGTGATGCATCCTCTCCCGAGCCACAGAACCAAAGAGTTTATAGAGGAATTTACAGCCTCGTTTTCATGTGATTGCTACATCCTAACAGGGCTTCATTTGGGGGTGGGGGGAAACATGTAAAAATAATTGCCAGTTTCTACTTTTCTATTAGCTTTTTAAAAATCAGCTGTAAAGTTGCATTTCTAAAGAAAGATATATATAATATATAAAATACATATATAGATCAACTTGACATTGGTGATAACCAAAATTATTGCTGTCCAAATTCATGTCTTGTTTTGGTCCAGTGCTTCATTTGCTAAGTATTCGGTTCAGAATTTTTCTCATTTCTCATGCCATTCCAGAGTTAATTTGCCACTGTGGATGATTTGAAGTATTCAGATCTCTATGGAAGTTTCTGGGACAGGTTTAAAGTCAAGATCAAGCATTTTAGCATTTAACCTGTTGATAAATGGATCCATGGTGTACATGAGTTTTATTTGTATTCGGAGTCATCTCTATTCTATCCCTCAGCCTCGATTAAGGTGGTGAGTGAAGTGCATCCAACAGACTCGGCCCAGAACTGGGTCCTGACAGTGGGGTGCTCATCTTCTGTAACTGTTGGGAAGGCTCGGTGGTCCATTTTCACCAGTTAAAGAATATGAGGCCAGCCCAGAAATCTGTTCTCCAGGAGCTGCCCTGTCCCATCTGGGTGTGCCAGACCCCCTCAGTGAGCAGGTCCACCAAAGGGACTTCTCACAGGGGAAGCCCAACTCCTGTTGCAATGGGTTGATAGATTTCCTCAGGGTGGTAATTACCAATTCGTATTTTGACAAGCCTATGTGCAACCACAGCTGGCACTGGGGTGGGCAGTGGTGTTGGGTGGGATGGGGGAGAGTGTCTCAATCCTGAAGAGAAAATATAAAGCAGGTTTTGGGGAGACTTCTGGAGTCCTGCCCCTAGAGAGCCCCATTGTTGTTCTTTGTGCCCCCTCCTCATTCCCCCTATGTGGGTCTCCCTATGCAGGAGCTGTGAGAGAATGTGACTCTCCACAATTTTTATAATTCATCCTTCCTAGGAGATTGTTCATTGGCTCTTCCCTTGTGTCCCTTTGTCCCTTGCTCATACTCCATGTTTCCTTTGTCAAAGGACTAAGAAAAGAGCATATTTCAGCAGAGGAGTGTTCCCATGTGGGTTGATTTCAACTTGGGTATTTCTAAAAGAGTCCTTGTGACATGTGTCCAGTGGAAATGGTTGCTCTTTTCCAGACTGGATTGAGGAATGGAGCCTGTTTGATTTGGTTAGTGATTCTTTGACATACTAATCTCAGCGTTTGGGTCTCCAGCATCCTCTGAAGATGTCTAGACTAGTAGAGGCTGCCTTTGTGACCTGACATTACAACATTGGTCAAACCAGTCCTCTGATAATCAGAAGAACATGTCATAATTGTTTAAAAAAAAAAAAAAGGCAAGAATTTCTCTCCAAGGAGCTTTAATAAATGTCTCATTCCAGATAATGTCATACCAGAGAAAAGTGCTTGCTTTTAGAAAATTATTTACATACATATATAAATATATATGTGTATCTATACAGTTATGTATCAAAATTTTAAGCCCTGCAGAATTTCAATTTGTTAGAAATCTAACAGAAAAAAATTTCTATATTGAAAGGTAATAGAATTTAACCCAGTGAGTTTACTCAAGGATTTTTAAATTTAAGTTAATAATTTCAGAGAAAATAACCATTTGGGTGTGGTTATAGTTTAGTATCCATTACCTCAATCCAAGGAAAATTCCAGGCATTCCTCAACCATCAGGAAAAGGTACAGTGTGAAGGAACAGTTCTCAGCCAAATTTCACATTCTTGAGGCAACAGAAATCAAAACACTCAGAGCCATTGAGTGGAAAAACAATTTACTTTATTCCTTTACACAAATAGGCTTGCATTGTTTTTGTTTTAATGTGATTTTGGTACTAGGGATATAATTATTTCATTCCAGGAAATAATAAAAAAAAACAGACAGAGCCAATACATTTCTTTTTTTAAAGGAAACAGCAACAACAATAAAAACTCAGCACCAATATTTAAAAGCTTTTCCAAAATGTAAAAGAAGTGTTTAGCTTGCACCATGCATAAAGGTGCAGGCTAGTTGAACCAGGAAGCATGGCACTTCCTCTGGAGAAATCCAGAAAGAGTTGCTTCTAAGCTCCCTTTTCCCCCTGCAGGCTCTTGGCAATTGTAGGCTTTAGCAAATCCAGAATAATTTTCAATTCAAGCTAAAATAAAATCAACATTTGGAATGTAAATCTGATACACACACACTTTTCTAAGTCAAACAACATATTTCAAAACCAAAAATAAATACCTTTTAGATAATCAGTTATTTTCTTTGTCTATACTGGGCACCCACCTACTAGTGCCAGTAAATTCAAGTTGAACAGATTTTTAAAATCACTATTATCTGGGTATGGGGGAAACTTCCCCACTTTTGAAAATGTTGGTAGAATTATAGGAATGTCTGTTTGATTATCATTACCAAAGTGTCATGACAGTATGCCTTTGTAGTGAACTCGGATTTTCAGGAGTTTGAATAGTTGGATATTTTAAAATCTAAGAAGAAAAGGCCTGTTTCCAATGTTGTTGAAGAATAATGAACTCTATTAAAAAGTGGAGAAAAAGATAATACATGTGGTCAAGGTTGACCACAAGGCCCAGGCACAACTACCTTGGCGATAATCTTCTAGATTCGTAACAGGTTAGAGCTGACTTTTTGTTTTTGTTGTTGCTGATGCTGTGTGATTCAGACTTCTCAGCCTAACCAGGAAGAGTAAGTGGAAATGGTAGATGAAGAAGGGGTAGAGCTGGTGTATCTATAACTTTCTGATATTTGTCTGCCAAACTTGATATATTAGTAATTTTTTTATCTTTAGCTAAGATCAAGTCACCCCTGAAACAACAGGAGATTCTAGTTTTAAAATAAGGCCACAAAAATCCTTACGGAATGAAGAATGGCACCCCAGTTGGTTGTATAAGTCTCATAAGATAATGATGTTGATTTTAAATATGGATGTCTCAATGCCTGTTTTCTATCAATGATTTGTTTGTTTCCAAGGTCGGGGAGGGAAAGAGGGGAGGGTTTATCTGTTTTAGAAAGTCTCAGAATACTTATAAAATACAGAAGTAGTTATTAAAATATATAGGACCTCACATAGGTAGATACAGAACTTACCATTGAGGCTGATGGGCTGTTGTGTGAATCACACAGGACCTTAAATGAGGCTCATTATTCTCACACACCAAAATGACTCTGACAGCCTGAAGCAGTTATTGCTAGAGCCCAAGCTTTCCTTGGAGGTTTTGGAGTTAGGTTGATTGGAAGTAACCAGCTAATACCTTTTCTAGTGGAGAAAAAGACATTGCTACCAGCTTGTTCATCCCATAGAAGTCTTCCACTCTGCTCCATTTTTAGCAGCAAGCATTTCATGTAGCATAAACCTTGGCAGATAAGTGTGCCTAAGGTTTATACAGTCTGTCCGCTTGGATGTATACAAATTTAGATACATATTTTAACATGTGTTCTCATAGATGACTTTATAACAACACACATTACCTATAGGTGTCTAGACTGTGTACATACAAGTGTGTACAGACAAGCTTCATACGTATATACTGTAATCCGTTACAACAAATAAATTTTAAATCATCGTTTAACATGTATGTGGTACTTCTACAGTGTACATTGTTTTCATTATTTATTGTAACATTGAAAACCACAGTGCAGGGAAAACAAAAGTATCCCAGCATCTTCATCCTGTACACTTGGAATTAATTTCATTTGGGCATATCCAAGATAAACTCAACTTTCAAGAAATCTTGTATATTATTTAATCATCTGTGTTAGGATGACACCTATGATTGATGACTTCGGTTGAATAGCTTTATTCTGGATTTTTCATAACTAAAGCTAAATCCAAAGACCTGAAAAAGGACAAAAAGAAAAAAAAAAAAAGAAA\"\n",
"a = a.upper()\n",
"a = a.replace(\"\\n\",\"\")\n",
" \n",
@@ -743,19 +559,9 @@
},
{
"cell_type": "code",
- "execution_count": 118,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL\n",
- "MVSC\n",
- "MCSEQHCFVDTSI\n"
- ]
- }
- ],
+ "outputs": [],
"source": [
"def translate(seq,orf):\n",
" seq = seq.upper()\n",
@@ -806,7 +612,7 @@
" \n",
" return protein\n",
"\n",
- "a = \"AGTGCGGAGCCTTAGGCGGAGCGAAGAGAACCGGTCGCGGCAATCCTAGCGCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCCGCATCCGCTGCGGGAGTCCGAGCCGGAACCACACCCAAGTAGCTGCCCTTTCCTCTTCTGTCATCTCACCGCCCCACCACAGACCGCGTTCCCCGAGGAAACCGGCCGCCCACGCCCGGAGCATCCTCCCCTGTTGAGCGGGCGCTGACGGACCCGGCGGCATGATGCGGCTGCGAGGCTCGGGGATGCTGCGGGACCTGCTCCTGCGGTCGCCCGCCGGCGTGAGCGCGACTCTGCGGCGGGCACAGCCCTTGGTCACCCTGTGCCGGCGTCCCCGAGGCGGGGGACGGCCGGCCGCGGGCCCGGCTGCCGCCGCGCGACTCCACCCGTGGTGGGGCGGGGGCGGCTGGCCGGCGGAGCCCCTCGCGCGGGGCCTGTCCAGCTCTCCTTCGGAGATCTTGCAGGAGCTGGGCAAGGGGAGCACGCATCCGCAGCCCGGGGTGTCGCCACCCGCTGCCCCGGCGGCGCCCGGCCCCAAGGACGGCCCCGGGGAGACGGACGCGTTTGGCAACAGCGAGGGCAAAGAGCTGGTGGCCTCAGGTGAAAATAAAATAAAACAGGGTCTGTTACCTAGCTTGGAAGATTTGCTGTTCTATACAATTGCTGAAGGACAAGAGAAAATACCTGTTCATAAATTTATTACAGCACTCAAATCTACAGGATTGCGAACGTCTGATCCCAGGTTGAAAGAGTGTATGGATATGTTAAGATTAACTCTTCAAACAACATCAGATGGTGTCATGCTAGACAAAGATCTTTTTAAAAAATGTGTTCAGAGCAACATTGTTTTGTTGACACAAGCATTTAGAAGAAAGTTTGTGATTCCTGACTTTATGTCTTTTACCTCACACATTGATGAGTTATATGAAAGTGCTAAAAAGCAGTCTGGAGGAAAGGTTGCAGATTATATTCCTCAACTGGCCAAATTCAGTCCCGATTTGTGGGGTGTGTCTGTTTGTACAGTAGATGGACAGAGGCATTCTACTGGAGATACCAAAGTTCCCTTCTGTCTTCAGTCCTGTGTAAAACCTTTGAAATATGCCATTGCTGTTAATGATCTTGGAACTGAATATGTGCATCGATATGTTGGAAAAGAGCCGAGTGGACTAAGATTCAACAAACTATTTTTGAATGAAGATGATAAACCACATAATCCTATGGTAAATGCTGGAGCAATTGTTGTGACTTCACTAATAAAGCAAGGAGTAAATAATGCTGAAAAATTTGACTATGTCATGCAGTTTTTGAATAAGATGGCTGGTAATGAATATGTTGGATTCAGTAATGCAACGTTTCAGTCTGAAAGAGAAAGTGGAGATCGAAATTTTGCAATAGGATATTACTTAAAAGAAAAGAAGTGTTTTCCAGAAGGCACAGACATGGTTGGTATATTAGACTTCTACTTCCAGCTGTGCTCCATTGAAGTGACTTGTGAATCAGCCAGTGTGATGGCTGCGACACTGGCTAATGGTGGTTTCTGCCCAATTACTGGTGAAAGAGTACTGAGCCCTGAAGCAGTTCGAAATACATTGAGTTTGATGCATTCCTGTGGCATGTATGACTTCTCAGGGCAGTTTGCTTTCCATGTTGGTCTTCCTGCAAAATCTGGAGTTGCTGGGGGCATTCTTTTAGTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTAAGGGAATTCACTTTTGTCACGATCTTGTTTCTCTGTGTAATTTCCATAACTATGATAATTTGAGACACTTTGCAAAAAAACTTGATCCTCGAAGAGAAGGTGGTGATCAAAGGGTAAAGTCAGTGATAAATCTTTTGTTTGCTGCATATACTGGAGATGTGTCTGCACTTCGAAGATTTGCTTTGTCAGCTATGGACATGGAACAGCGGGACTATGATTCTAGAACAGCACTCCATGTAGCTGCTGCAGAGGGTCATGTTGAAGTTGTTAAATTTTTGCTGGAAGCCTGCAAAGTAAACCCTTTCCCCAAGGACAGGTGGAATAACACTCCCATGGATGAAGCACTGCACTTTGGACACCATGATGTATTTAAAATTCTCCAAGAATACCAAGTCCAGTACACACCTCAAGGAGATTCTGACAACGGGAAGGAAAATCAAACCGTCCATAAGAATCTTGATGGATTGTTGT\"\n",
+ "a = \"TGGACAGCTCCCGCTCACCCAAACAGAAGACGTCGGCGCCGGAGCGGGCTCGGACATGGCGAGGCTGCGAGCCGGCCCGAGCGGCGGGGCCCGGTGATCCCTCCCTCCCTCCCCGTCCCCTCCCCTCTCCCGCACGCACGCCCCGTCCGCCCCCACCCCGCCCCCACCCCGGGCGAGCCCGCCCGCAGCCCGGGGCGCACACCCGCACGCGCACTCCTCTCCACTCACTCCCGCGCCCGCCCCCACTCCCGCAGCCGAGCCCCGCCACGCGCGCCTTGCCCGCCCGCCGGCCGCCCCCGCCGCCCCCGCCGCCCCCGGGCCCTGATGGACTGAATGAAGGCTGCCTACACCGCCTATCGATGCCTCACCAAAGACCTAGAAGGCTGCGCCATGAACCCGGAGCTGACAATGGAAAGTCTGGGCACTTTGCACGGGCCGGCCGGCGGCGGCAGTGGCGGGGGCGGCGGCGGGGGCGGCGGGGGCGGCGGCGGGGGCCCGGGCCATGAGCAGGAGCTGCTGGCCAGCCCCAGCCCCCACCACGCGGGCCGCGGCGCCGCTGGCTCGCTGCGGGGCCCTCCGCCGCCTCCAACCGCGCACCAGGAGCTGGGCACGGCGGCAGCGGCGGCAGCGGCGGCGTCGCGCTCGGCCATGGTCACCAGCATGGCCTCGATCCTGGACGGCGGCGACTACCGGCCCGAGCTCTCCATCCCGCTGCACCACGCCATGAGCATGTCCTGCGACTCGTCTCCGCCTGGCATGGGCATGAGCAACACCTACACCACGCTGACACCGCTCCAGCCGCTGCCACCCATCTCCACCGTGTCTGACAAGTTCCACCACCCTCACCCGCACCACCATCCGCACCACCACCACCACCACCACCACCAGCGCCTGTCCGGCAACGTCAGCGGCAGCTTCACCCTCATGCGCGACGAGCGCGGGCTCCCGGCCATGAACAACCTCTACAGTCCCTACAAGGAGATGCCCGGCATGAGCCAGAGCCTGTCCCCGCTGGCCGCCACGCCGCTGGGCAACGGGCTAGGCGGCCTCCACAACGCGCAGCAGAGTCTGCCCAACTACGGTCCGCCGGGCCACGACAAAATGCTCAGCCCCAACTTCGACGCGCACCACACTGCCATGCTGACCCGCGGTGAGCAACACCTGTCCCGCGGCCTGGGCACCCCACCTGCGGCCATGATGTCGCACCTGAACGGCCTGCACCACCCGGGCCACACTCAGTCTCACGGGCCGGTGCTGGCACCCAGTCGCGAGCGGCCACCCTCGTCCTCATCGGGCTCGCAGGTGGCCACGTCGGGCCAGCTGGAAGAAATCAACACCAAAGAGGTGGCCCAGCGCATCACAGCGGAGCTGAAGCGCTACAGTATCCCCCAGGCGATCTTTGCGCAGAGGGTGCTGTGCCGGTCTCAGGGGACTCTCTCCGACCTGCTCCGGAATCCAAAACCGTGGAGTAAACTCAAATCTGGCAGGGAGACCTTCCGCAGGATGTGGAAGTGGCTTCAGGAGCCCGAGTTCCAGCGCATGTCCGCCTTACGCCTGGCAGCGTGCAAACGCAAAGAGCAAGAACCAAACAAAGACAGGAACAATTCCCAGAAGAAGTCCCGCCTGGTGTTCACTGACCTCCAACGCCGAACACTCTTCGCCATCTTCAAGGAGAACAAACGCCCGTCAAAGGAGATGCAGATCACCATTTCCCAGCAGCTGGGCCTGGAGCTCACAACCGTCAGCAACTTCTTCATGAACGCCCGGCGCCGCAGCCTGGAGAAGTGGCAAGACGATCTGAGCACAGGGGGCTCCTCGTCCACCTCCAGCACGTGTACCAAAGCATGATGGAAGGACTCTCACTTGGGCACAAGTCACCTCCAAATGAGGACAACAGATACCAAAAGAAAACAAAGGAAAAAGACACCGGATTCCTAGCTGGGGCCCTTCACTGGTGATTTGAAAGCACAATTCTCTTGCAAAGAAACTTATATTCTAGCTGTAATCATAGGCCAGGTGTTCTTCTTTTGTTTTTAATGGCTATGGAGTCCAAGTGCAAGCTGAAAAATTAATCTCTTAGAACCAGACACTGTTCTCTGAGCATGCTAAGCATCCCAGAAACCCAAATGGGGCCTTCCTGGAGCGAGTTAATTCCAGTATGGTGTCAACCAAGCTCGGGATTGCTTAAAATATCATCCATCCCACTTCAGGTCCTGTCAGCTTCTTGCAGTCAGAGTTCCTATGAGTAACAATAGGAGTTTGGCCTATGTAAGGACTCTGAGTTTAGGCTTCCAAGATACAACAATAAGAGAAGAATCTAGCAACGAGAATGACCTCATTTGCTTTCCACATGCTTAGCCTCATTATACCATGTTATGTCCAAGTTCACAGCCACAACATCAGAATGGTAATTACTGAGCACAAGTTTTAAATATGGACGTTAAAAAAAAAAATCCAAGGACCTGTTTTTCCAACCCAGACATCTTTTCATTGAATGATTTAGAAAGCTTTAAGTTGATCCAGCTTACAATTTTTTTTTTCTTTACCTCCTGGAAATCTCATATGGTCTTGGATCCGTCAAAAAAACCAGTCAGTTCACTTGCGCTCAAAGTATCAAGCACAACAAAGATAAACAGAAGTGAGGAAGGTTCTGGGTTCACTACATCTGGATTTTCAAGACACCTATTGTGAAGTCATTAGGGAATTGATGAGAATATGGCTTCAAGCACATTTTGCAGTTTGCTACAAATTCTGTTGTACATAATGCAGACGCACACTCAGGAGGCCAATTTAACTGTTAACAGTGCATGGAGCGAATGCAGCATTTTAAAAGATCTAGGTTTTTTTAGGTCATTAATGTGTCCTTGGTTGATCAGTCATCTGGTCCCTCCTACTGTGTGTTATGACCACCACGTAATCCATTCTCGCTCTTTCTGATTTGGGGTTTTTCCTCATCCATCCCATTAGTAGGGATGTTTTCTGTGTTTTCTAGCAAGAAAAAAAAATCAATCAATCAAACCTGCATACATGTTACTCATGACTGTCATCTAGTCCTAAATCTCTTCTGTTGTTGAATCATCCTTGCAAAACAGCTGAATACATCTGGAGAAAACACAGCACACCAAAGAAGCAGAATACTGCAAACCAAAGACATTTATGACTTGTCATTTTCTAGCCTAAAAATACTGTGATTACTTTTAGAAATCAGAAAACCTCTGCAACTCCGAATGGCATTCAGCTCTTGCATTTGGCGCATCATCGGGCTGAGCGGACCAGCTACACCAAGGACATTAGCCAAGCCACCCAGAGGGGTGGCTTTGCCACACCAGTTGTCACCTTCCCATAGCAAGTGGAAGAGCGCCCACAGAACTCTGGGAGATTGCAAAGGTCACAATGTGCATATTTACCAGTGAATGGCCCCGGGTGGGGCCACGTGGGGGTGTTCAAAGCAAGCCAAACGCTGCAATCATTCTTTACAGACACTTGAGACTGACTTTTTTATGAATTACTTAGTCGAAACCAAAGAAACTTTTTCTGCACCTACTTCTGCAACAAACAAAACTGTCCCATTAAAATGAATAAATAAATCCGTAAATCAATGGAAATCACCACCAATAAGAAGGAAGCACGCCAGAAAATAAACGAAAACAAAAACAGGGAGACACACTGTGTTCAAACAGACCTCTTGGGACATTTTTTGGAAGCAGATTTTAAAGAAAGGGTTGAGACAAAGATAGAAATAAGGAAGAGCCTCAGTGGCTGCTGCTTCATTTGACAACTCACACGGTAATCTTAAAGCTGAAGATTGTCTTTAATTTGTGCCTATGCAGTTTTTCAAAAGAACACGGAACAGAGCAACAGAAACCTCAACAGCTACAATACCAAAGATGAGGATTTCTCACACCTTTTGTTTCAGTTCATTATCTCCTCTTGCCTGGCTAAAATACTAATAGCGCCATTGAACTGTATAAAGGTAATCAATTATGTTTCTCTGAGCAACAAAAGGAAAGGGCCATTTATTTGATTTTATTGTTTCATTTCAATTTTGTCTTATGGTTTTTTGCCCCAACATGGAATCTCTCAAAAGTTTCCATGGACTCCAAGTTTAAGATGTTGGGATATTGAACAGTTCTCTCTGCTCAGCAGAGGGTAGGGAATAACATTATCACTTGAATGTTCTTTGCTTAACCCTTAGACTTGGTTCCTTCTATGTTCAGAGTCTCATCATCAGGGGAAGGAAAGGGAGTGAGGGTCAGGGATAGGGGTCTTGGTGATGCATCCTCTCCCGAGCCACAGAACCAAAGAGTTTATAGAGGAATTTACAGCCTCGTTTTCATGTGATTGCTACATCCTAACAGGGCTTCATTTGGGGGTGGGGGGAAACATGTAAAAATAATTGCCAGTTTCTACTTTTCTATTAGCTTTTTAAAAATCAGCTGTAAAGTTGCATTTCTAAAGAAAGATATATATAATATATAAAATACATATATAGATCAACTTGACATTGGTGATAACCAAAATTATTGCTGTCCAAATTCATGTCTTGTTTTGGTCCAGTGCTTCATTTGCTAAGTATTCGGTTCAGAATTTTTCTCATTTCTCATGCCATTCCAGAGTTAATTTGCCACTGTGGATGATTTGAAGTATTCAGATCTCTATGGAAGTTTCTGGGACAGGTTTAAAGTCAAGATCAAGCATTTTAGCATTTAACCTGTTGATAAATGGATCCATGGTGTACATGAGTTTTATTTGTATTCGGAGTCATCTCTATTCTATCCCTCAGCCTCGATTAAGGTGGTGAGTGAAGTGCATCCAACAGACTCGGCCCAGAACTGGGTCCTGACAGTGGGGTGCTCATCTTCTGTAACTGTTGGGAAGGCTCGGTGGTCCATTTTCACCAGTTAAAGAATATGAGGCCAGCCCAGAAATCTGTTCTCCAGGAGCTGCCCTGTCCCATCTGGGTGTGCCAGACCCCCTCAGTGAGCAGGTCCACCAAAGGGACTTCTCACAGGGGAAGCCCAACTCCTGTTGCAATGGGTTGATAGATTTCCTCAGGGTGGTAATTACCAATTCGTATTTTGACAAGCCTATGTGCAACCACAGCTGGCACTGGGGTGGGCAGTGGTGTTGGGTGGGATGGGGGAGAGTGTCTCAATCCTGAAGAGAAAATATAAAGCAGGTTTTGGGGAGACTTCTGGAGTCCTGCCCCTAGAGAGCCCCATTGTTGTTCTTTGTGCCCCCTCCTCATTCCCCCTATGTGGGTCTCCCTATGCAGGAGCTGTGAGAGAATGTGACTCTCCACAATTTTTATAATTCATCCTTCCTAGGAGATTGTTCATTGGCTCTTCCCTTGTGTCCCTTTGTCCCTTGCTCATACTCCATGTTTCCTTTGTCAAAGGACTAAGAAAAGAGCATATTTCAGCAGAGGAGTGTTCCCATGTGGGTTGATTTCAACTTGGGTATTTCTAAAAGAGTCCTTGTGACATGTGTCCAGTGGAAATGGTTGCTCTTTTCCAGACTGGATTGAGGAATGGAGCCTGTTTGATTTGGTTAGTGATTCTTTGACATACTAATCTCAGCGTTTGGGTCTCCAGCATCCTCTGAAGATGTCTAGACTAGTAGAGGCTGCCTTTGTGACCTGACATTACAACATTGGTCAAACCAGTCCTCTGATAATCAGAAGAACATGTCATAATTGTTTAAAAAAAAAAAAAAGGCAAGAATTTCTCTCCAAGGAGCTTTAATAAATGTCTCATTCCAGATAATGTCATACCAGAGAAAAGTGCTTGCTTTTAGAAAATTATTTACATACATATATAAATATATATGTGTATCTATACAGTTATGTATCAAAATTTTAAGCCCTGCAGAATTTCAATTTGTTAGAAATCTAACAGAAAAAAATTTCTATATTGAAAGGTAATAGAATTTAACCCAGTGAGTTTACTCAAGGATTTTTAAATTTAAGTTAATAATTTCAGAGAAAATAACCATTTGGGTGTGGTTATAGTTTAGTATCCATTACCTCAATCCAAGGAAAATTCCAGGCATTCCTCAACCATCAGGAAAAGGTACAGTGTGAAGGAACAGTTCTCAGCCAAATTTCACATTCTTGAGGCAACAGAAATCAAAACACTCAGAGCCATTGAGTGGAAAAACAATTTACTTTATTCCTTTACACAAATAGGCTTGCATTGTTTTTGTTTTAATGTGATTTTGGTACTAGGGATATAATTATTTCATTCCAGGAAATAATAAAAAAAAACAGACAGAGCCAATACATTTCTTTTTTTAAAGGAAACAGCAACAACAATAAAAACTCAGCACCAATATTTAAAAGCTTTTCCAAAATGTAAAAGAAGTGTTTAGCTTGCACCATGCATAAAGGTGCAGGCTAGTTGAACCAGGAAGCATGGCACTTCCTCTGGAGAAATCCAGAAAGAGTTGCTTCTAAGCTCCCTTTTCCCCCTGCAGGCTCTTGGCAATTGTAGGCTTTAGCAAATCCAGAATAATTTTCAATTCAAGCTAAAATAAAATCAACATTTGGAATGTAAATCTGATACACACACACTTTTCTAAGTCAAACAACATATTTCAAAACCAAAAATAAATACCTTTTAGATAATCAGTTATTTTCTTTGTCTATACTGGGCACCCACCTACTAGTGCCAGTAAATTCAAGTTGAACAGATTTTTAAAATCACTATTATCTGGGTATGGGGGAAACTTCCCCACTTTTGAAAATGTTGGTAGAATTATAGGAATGTCTGTTTGATTATCATTACCAAAGTGTCATGACAGTATGCCTTTGTAGTGAACTCGGATTTTCAGGAGTTTGAATAGTTGGATATTTTAAAATCTAAGAAGAAAAGGCCTGTTTCCAATGTTGTTGAAGAATAATGAACTCTATTAAAAAGTGGAGAAAAAGATAATACATGTGGTCAAGGTTGACCACAAGGCCCAGGCACAACTACCTTGGCGATAATCTTCTAGATTCGTAACAGGTTAGAGCTGACTTTTTGTTTTTGTTGTTGCTGATGCTGTGTGATTCAGACTTCTCAGCCTAACCAGGAAGAGTAAGTGGAAATGGTAGATGAAGAAGGGGTAGAGCTGGTGTATCTATAACTTTCTGATATTTGTCTGCCAAACTTGATATATTAGTAATTTTTTTATCTTTAGCTAAGATCAAGTCACCCCTGAAACAACAGGAGATTCTAGTTTTAAAATAAGGCCACAAAAATCCTTACGGAATGAAGAATGGCACCCCAGTTGGTTGTATAAGTCTCATAAGATAATGATGTTGATTTTAAATATGGATGTCTCAATGCCTGTTTTCTATCAATGATTTGTTTGTTTCCAAGGTCGGGGAGGGAAAGAGGGGAGGGTTTATCTGTTTTAGAAAGTCTCAGAATACTTATAAAATACAGAAGTAGTTATTAAAATATATAGGACCTCACATAGGTAGATACAGAACTTACCATTGAGGCTGATGGGCTGTTGTGTGAATCACACAGGACCTTAAATGAGGCTCATTATTCTCACACACCAAAATGACTCTGACAGCCTGAAGCAGTTATTGCTAGAGCCCAAGCTTTCCTTGGAGGTTTTGGAGTTAGGTTGATTGGAAGTAACCAGCTAATACCTTTTCTAGTGGAGAAAAAGACATTGCTACCAGCTTGTTCATCCCATAGAAGTCTTCCACTCTGCTCCATTTTTAGCAGCAAGCATTTCATGTAGCATAAACCTTGGCAGATAAGTGTGCCTAAGGTTTATACAGTCTGTCCGCTTGGATGTATACAAATTTAGATACATATTTTAACATGTGTTCTCATAGATGACTTTATAACAACACACATTACCTATAGGTGTCTAGACTGTGTACATACAAGTGTGTACAGACAAGCTTCATACGTATATACTGTAATCCGTTACAACAAATAAATTTTAAATCATCGTTTAACATGTATGTGGTACTTCTACAGTGTACATTGTTTTCATTATTTATTGTAACATTGAAAACCACAGTGCAGGGAAAACAAAAGTATCCCAGCATCTTCATCCTGTACACTTGGAATTAATTTCATTTGGGCATATCCAAGATAAACTCAACTTTCAAGAAATCTTGTATATTATTTAATCATCTGTGTTAGGATGACACCTATGATTGATGACTTCGGTTGAATAGCTTTATTCTGGATTTTTCATAACTAAAGCTAAATCCAAAGACCTGAAAAAGGACAAAAAGAAAAAAAAAAAAAGAAA\"\n",
"print(translate(a,0))\n",
"print(translate(a,1))\n",
"print(translate(a,2))"
@@ -814,25 +620,23 @@
},
{
"cell_type": "code",
- "execution_count": 160,
+ "execution_count": 9,
"metadata": {},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "264 CGGCATGA MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL 0.003137706\n"
+ "ename": "FileNotFoundError",
+ "evalue": "[Errno 2] No such file or directory: '/home/annaldas/projects/result/ONECUT2/ONECUT2_seq.fa'",
+ "output_type": "error",
+ "traceback": [
+ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+ "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)",
+ "\u001b[0;32m<ipython-input-9-28170ef6fa91>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 125\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 126\u001b[0m \u001b[0mtranscripts_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"/home/annaldas/projects/result/ONECUT2/ONECUT2_seq.fa\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 127\u001b[0;31m \u001b[0mtranscripts\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mSeqIO\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mindex\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mtranscripts_filename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"fasta\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 128\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 129\u001b[0m \u001b[0mgene\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"ONECUT2\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/pkg/python-3.7.4-0/lib/python3.7/site-packages/Bio/SeqIO/__init__.py\u001b[0m in \u001b[0;36mindex\u001b[0;34m(filename, format, alphabet, key_function)\u001b[0m\n\u001b[1;32m 951\u001b[0m \u001b[0mrepr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"SeqIO.index(%r, %r, alphabet=%r, key_function=%r)\"\u001b[0m\u001b[0;31m \u001b[0m\u001b[0;31m\\\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 952\u001b[0m \u001b[0;34m%\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malphabet\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkey_function\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 953\u001b[0;31m return _IndexedSeqFileDict(proxy_class(filename, format, alphabet),\n\u001b[0m\u001b[1;32m 954\u001b[0m key_function, repr, \"SeqRecord\")\n\u001b[1;32m 955\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/pkg/python-3.7.4-0/lib/python3.7/site-packages/Bio/SeqIO/_index.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, filename, format, alphabet)\u001b[0m\n\u001b[1;32m 183\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malphabet\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 184\u001b[0m \u001b[0;34m\"\"\"Initialize the class.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 185\u001b[0;31m \u001b[0mSeqFileRandomAccess\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malphabet\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 186\u001b[0m marker = {\"ace\": b\"CO \",\n\u001b[1;32m 187\u001b[0m \u001b[0;34m\"embl\"\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34mb\"ID \"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/pkg/python-3.7.4-0/lib/python3.7/site-packages/Bio/SeqIO/_index.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, filename, format, alphabet)\u001b[0m\n\u001b[1;32m 44\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0m__init__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0malphabet\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 45\u001b[0m \u001b[0;34m\"\"\"Initialize the class.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 46\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_handle\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_open_for_random_access\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 47\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_alphabet\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0malphabet\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 48\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_format\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mformat\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;32m/pkg/python-3.7.4-0/lib/python3.7/site-packages/Bio/File.py\u001b[0m in \u001b[0;36m_open_for_random_access\u001b[0;34m(filename)\u001b[0m\n\u001b[1;32m 130\u001b[0m \u001b[0mIf\u001b[0m \u001b[0mthe\u001b[0m \u001b[0mfile\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mgzipped\u001b[0m \u001b[0mbut\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mBGZF\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0ma\u001b[0m \u001b[0mspecific\u001b[0m \u001b[0mValueError\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0mraised\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 131\u001b[0m \"\"\"\n\u001b[0;32m--> 132\u001b[0;31m \u001b[0mhandle\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfilename\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"rb\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 133\u001b[0m \u001b[0mmagic\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mhandle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 134\u001b[0m \u001b[0mhandle\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mseek\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+ "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '/home/annaldas/projects/result/ONECUT2/ONECUT2_seq.fa'"
]
- },
- {
- "data": {
- "text/plain": [
- "'MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL'"
- ]
- },
- "execution_count": 160,
- "metadata": {},
- "output_type": "execute_result"
}
],
"source": [
@@ -888,13 +692,13 @@
" translating = True\n",
" aa = \"\"\n",
" \n",
+ " in_utr = False\n",
+ " for utr in utr_regions:\n",
+ " start,stop = utr\n",
+ " if ((start < i) and (i < stop)):\n",
+ " in_utr = True\n",
+ " \n",
" while(translating): \n",
- " in_utr = False\n",
- " for utr in utr_regions:\n",
- " start,stop = utr\n",
- " if ((start < i) and (i < stop)):\n",
- " in_utr = True\n",
- " \n",
" if ((len(seq) < 3) or (in_utr)):\n",
" translating = False\n",
" aa = \"\"\n",
@@ -906,47 +710,80 @@
" aa += codon_table[codon]\n",
" seq = seq[3:]\n",
" i += 3\n",
- " return aa\n",
+ " return aa,i\n",
"\n",
+ "def find_utrs(seq,utr):\n",
+ " pos = seq.find(utr)\n",
+ " if (pos == -1):\n",
+ " if (len(utr) > 20): \n",
+ " for i in range(len(utr) - 1,len(utr)*5//10 - 1,-1):\n",
+ " pos = seq.find(utr[:i])\n",
+ " return pos\n",
"\n",
"def translate_aa_seq(seq,enst,gene_utrs):\n",
" utr_regions = []\n",
" for utr in gene_utrs[enst]:\n",
- " pos = seq.find(utr)\n",
+ " pos = find_utrs(seq,utr)\n",
" if (pos != -1):\n",
" utr_regions.append([pos,pos + len(utr)])\n",
" \n",
- " longest_aa_seq = \"\"\n",
+ " longest_aa_seq = \"M\"\n",
" longest_aa_seq_sc = 0\n",
+ " longest_aa_seq_sc_end = 0\n",
" for i in range(len(seq)):\n",
" if (seq[i:i+3] == \"ATG\"):\n",
" sc = score(seq[i-4:i+4],0)\n",
- " aa = translate(seq[i:], i, utr_regions)\n",
- " if ((aa != \"\") and (sc > longest_aa_seq_sc) and (aa not in longest_aa_seq)):\n",
- " print(i,seq[i-4:i+4],aa,sc)\n",
+ " aa,end = translate(seq[i:], i, utr_regions)\n",
+ " #print(i,seq[i-4:i+4],aa,sc, end)\n",
+ " if ((len(aa) > 20) and (sc > longest_aa_seq_sc) and (i > longest_aa_seq_sc_end)):\n",
" longest_aa_seq = aa\n",
" longest_aa_seq_sc = sc\n",
+ " longest_aa_seq_sc_end = end\n",
" return (longest_aa_seq,longest_aa_seq_sc)\n",
"\n",
- "def find_all_aa_seqs(seq,enst):\n",
- " gene_utrs = determine_utrs(\"GLS\")\n",
+ "\n",
+ "\n",
+ "def translate_aa_seq_length(seq,enst,gene_utrs):\n",
+ " utr_regions = []\n",
" \n",
- " if (enst in gene_utrs):\n",
- " longest_aa_seq,longest_aa_seq_sc = translate_aa_seq(seq,enst,gene_utrs)\n",
- " else:\n",
- " longest_aa_seq = \"\"\n",
- " longest_aa_seq_sc = 0\n",
- " for enst_id in gene_utr:\n",
- " aa_seq,aa_seq_sc = translate_aa_seq(seq,enst_id,gene_utrs)\n",
- " if (aa_seq_sc > longest_aa_seq_sc):\n",
- " longest_aa_seq = aa_seq\n",
- " longest_aa_seq_sc = aa_seq_sc\n",
+ " longest_aa_seq = \"M\"\n",
+ " for i in range(len(seq)):\n",
+ " if (seq[i:i+3] == \"ATG\"):\n",
+ " aa,end = translate(seq[i:], i, utr_regions)\n",
+ " #print(i,seq[i-4:i+4],aa, end)\n",
+ " if (len(aa) > len(longest_aa_seq)):\n",
+ " longest_aa_seq = aa\n",
+ " return longest_aa_seq\n",
+ "\n",
+ "def find_all_aa_seqs(seq,enst,gene):\n",
+ " gene_utrs = determine_utrs(gene)\n",
+ " \n",
+ " longest_aa_seq = translate_aa_seq_length(seq,enst,gene_utrs)\n",
+ " if gene in gene_utrs:\n",
+ " for utr in gene_utrs[gene]:\n",
+ " if (find_utrs(seq,utr) != -1):\n",
+ " longest_aa_seq,longest_aa_seq_sc = translate_aa_seq(seq,enst,gene_utrs)\n",
" \n",
" return longest_aa_seq\n",
" \n",
- "enst = \"ENST00000320717\"\n",
- "a=\"AGTGCGGAGCCTTAGGCGGAGCGAAGAGAACCGGTCGCGGCAATCCTAGCGCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCCGCATCCGCTGCGGGAGTCCGAGCCGGAACCACACCCAAGTAGCTGCCCTTTCCTCTTCTGTCATCTCACCGCCCCACCACAGACCGCGTTCCCCGAGGAAACCGGCCGCCCACGCCCGGAGCATCCTCCCCTGTTGAGCGGGCGCTGACGGACCCGGCGGCATGATGCGGCTGCGAGGCTCGGGGATGCTGCGGGACCTGCTCCTGCGGTCGCCCGCCGGCGTGAGCGCGACTCTGCGGCGGGCACAGCCCTTGGTCACCCTGTGCCGGCGTCCCCGAGGCGGGGGACGGCCGGCCGCGGGCCCGGCTGCCGCCGCGCGACTCCACCCGTGGTGGGGCGGGGGCGGCTGGCCGGCGGAGCCCCTCGCGCGGGGCCTGTCCAGCTCTCCTTCGGAGATCTTGCAGGAGCTGGGCAAGGGGAGCACGCATCCGCAGCCCGGGGTGTCGCCACCCGCTGCCCCGGCGGCGCCCGGCCCCAAGGACGGCCCCGGGGAGACGGACGCGTTTGGCAACAGCGAGGGCAAAGAGCTGGTGGCCTCAGGTGAAAATAAAATAAAACAGGGTCTGTTACCTAGCTTGGAAGATTTGCTGTTCTATACAATTGCTGAAGGACAAGAGAAAATACCTGTTCATAAATTTATTACAGCACTCAAATCTACAGGATTGCGAACGTCTGATCCCAGGTTGAAAGAGTGTATGGATATGTTAAGATTAACTCTTCAAACAACATCAGATGGTGTCATGCTAGACAAAGATCTTTTTAAAAAATGTGTTCAGAGCAACATTGTTTTGTTGACACAAGCATTTAGAAGAAAGTTTGTGATTCCTGACTTTATGTCTTTTACCTCACACATTGATGAGTTATATGAAAGTGCTAAAAAGCAGTCTGGAGGAAAGGTTGCAGATTATATTCCTCAACTGGCCAAATTCAGTCCCGATTTGTGGGGTGTGTCTGTTTGTACAGTAGATGGACAGAGGCATTCTACTGGAGATACCAAAGTTCCCTTCTGTCTTCAGTCCTGTGTAAAACCTTTGAAATATGCCATTGCTGTTAATGATCTTGGAACTGAATATGTGCATCGATATGTTGGAAAAGAGCCGAGTGGACTAAGATTCAACAAACTATTTTTGAATGAAGATGATAAACCACATAATCCTATGGTAAATGCTGGAGCAATTGTTGTGACTTCACTAATAAAGCAAGGAGTAAATAATGCTGAAAAATTTGACTATGTCATGCAGTTTTTGAATAAGATGGCTGGTAATGAATATGTTGGATTCAGTAATGCAACGTTTCAGTCTGAAAGAGAAAGTGGAGATCGAAATTTTGCAATAGGATATTACTTAAAAGAAAAGAAGTGTTTTCCAGAAGGCACAGACATGGTTGGTATATTAGACTTCTACTTCCAGCTGTGCTCCATTGAAGTGACTTGTGAATCAGCCAGTGTGATGGCTGCGACACTGGCTAATGGTGGTTTCTGCCCAATTACTGGTGAAAGAGTACTGAGCCCTGAAGCAGTTCGAAATACATTGAGTTTGATGCATTCCTGTGGCATGTATGACTTCTCAGGGCAGTTTGCTTTCCATGTTGGTCTTCCTGCAAAATCTGGAGTTGCTGGGGGCATTCTTTTAGTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTAAGGGAATTCACTTTTGTCACGATCTTGTTTCTCTGTGTAATTTCCATAACTATGATAATTTGAGACACTTTGCAAAAAAACTTGATCCTCGAAGAGAAGGTGGTGATCAAAGGGTAAAGTCAGTGATAAATCTTTTGTTTGCTGCATATACTGGAGATGTGTCTGCACTTCGAAGATTTGCTTTGTCAGCTATGGACATGGAACAGCGGGACTATGATTCTAGAACAGCACTCCATGTAGCTGCTGCAGAGGGTCATGTTGAAGTTGTTAAATTTTTGCTGGAAGCCTGCAAAGTAAACCCTTTCCCCAAGGACAGGTGGAATAACACTCCCATGGATGAAGCACTGCACTTTGGACACCATGATGTATTTAAAATTCTCCAAGAATACCAAGTCCAGTACACACCTCAAGGAGATTCTGACAACGGGAAGGAAAATCAAACCGTCCATAAGAATCTTGATGGATTGTTGTAATGGTCTCAAATCCCAAGATTTAAATCACTTACCTATTTAATTGTGGAAAATGATTATGAAGAACATGTGTATTTCTATCTGGTAGTGATGTATATTTTACATTTGTCATTTCAGTGTTACTGGAGTTTTCTTCATTGTGCACACAGGACAAATCTGATCTCTTTGGGAAAAAATAGAAATAAAACAATCTCCCTCCATAATGTGAGCAATATTACCTCGTGCATTGTATAATTTGATGTAAAAGAAATAGTTACCAATGCTAGCTTGTGTGGTCTTCCATGATTTATTTGTGTTTTGTGAATTTTCAATTTATGGTGATGATCTGCTGATATGCATTTATAAAGTAAGCTCTGTTGTACAGTCTGTCCAAATGGGTCAAGGTTGCCTTTAGAAGCAAATAGTGTGATTTTCAAGACTTCAAATACAAATTTAGTTTAAGTGTTTGAACAACTATATGCACTTACGGTTGTGTGTTTAAAATGTCTCTCTCACCCCCTAGCTTCATGATGTGACTCTTAAAAAACTATAATAGTTAACAACTGTTAGTAAGATAGACCAATTCTGATTAGACTTTATCAGGGAATCTGTTTAAGATATGTTTGGTGACCAAAACGTATGTGTGAATGTAGTTATAATGCTTTTGAAAAATTTTCCTTTTTCTATATCCCCTTAGTCCAGCCTCTCTTCTCAGACATTTAGCTATCTGCCTCTTTCCTTTAGCTGGGAAAGTGAGAGCTGGCATACTATGCAGTTTTTATGTTTTCCATAGTAAGTCAGAAAATGCCTCCTATTTCTGGCATCAGAACTTTGCCATTTGTCTACAGAAGACGAACCAGAGACAAAATTACTAAGTATAAATTAGTCAAGTTTATCAGTCTAAAAAACGAAGGGATGTGCAACTGCAGCTCTTTAAGAAGTTTTTTTTTTTTAGCTTCTAGGGTAAAGATAAATTCAGAAATGCTCTAAGCTACCAAAGTTATTCTGAAAGTATGGGAACTGCTACAACTAACAAACATTTGTTTCCAAGCCTGTCATTAAGAGTCTGCATCAAGAGATTTGTCCTCCTTGGGGGACCACTGGATCATTCCAGATTTCTTGTGATTTTTCTATTGTGTAATTCTTGGTGGGCTCTGTAGTTTAATAATAAGAAAAAGGCCATTTCATTTTAAATTGTGACCTATAATTCTTTGTCTTGGGTTGGTAATTCAGGATTCATTTGGAAAGTGGGTAAAAGGGGCTTCAAAAAACGGATAGAACAGGATTTTCTAGGAGTTACACATACATTTTATCCTGTCATACCTCGAGATAAAGTGGCATGTTAGTGAGGAGTTCTGATATTAAGCACACACACACATGCACACAAATGGACTTCTCTGAAGCTGTGTTTAGTGAAATGAGCTCAAGTACATGAATGTTAGTTGTTATCACATACAGCAAATTCCTTTTTTTTTCTTTTTCTATGAGCACACTCTGCTGCTTCTAAACTTTACATGCCTGATGGCACCTTACTCCAGCAGCCTCCAGGTGCTTTCATTTTCACTTCCAGTCTAAGCCAGTGGCTCCTGCCACTGCCCTCCCATTACCTAGATGGCACCTCCTTTGGTGAAACCACGGCCAATGTTCCTTAGCTGCACCAGGCCCGAAGCTGTTCCCATGCTTGAGCTTCCATGGGGAGGATGCTGAGTGAGCAGTTTCCTACCCCGTGGATCTAGCAAGCCATGGAGACAGGTAGCATTTGTAAGATGCTGCACAGGAGCAGCATTATCCCCAAAGATATTACAGGGTAGACACGTTTTAACTGAAATCAATCAAGATAACTTTATTCAAAGAGCAGCCCGCTTTGTGTGACTAAAATGAAACAAGACAGTTGAATTGTGTGACTTGAAGATTACCAATGATTTTGAGGCTTTTCTATAATAAAAAGAGGTTCTAACCATTATTTGGGAACAAAGAGAGTTTTCATCTTTTTTCAGATCAAAACCATTCTGTAAAATCTTTGTTGTTTAATTAAATGTGCCGTTATTTACCCCTGATGTTATTTATGACTATGTGCCGATTCCTGCTCGGGCTGTTTGCTGTTGGCTGGTAATAATATATTTGATTTAAATGCTGTTGACTGTGCTATTAACTGCTGCCGTCAGTAAACTCCAAAGATCTTTTTGTTTTGGCTTTAGTATCATATGTGCTTTTTCTGTATCCTGAGCGCTCTATATGATCATGTTAATTTAAAGCTTTATACACATTGTTGTTTTTGCTGGTCTCATCTTTGGTAATATGCTATACCCCACTGCTGCCCGACACTGCCCTTTAGCTGCAGAGCTGGATTAGCTGTTGACCATTTGATGCTGTTGTCTGTCTGGCAGGGACTGAATGACCTGATGTCAGATTTAGATTCTTCCTGGGGATTACACAGCTATGAATGTATTTGCTTCTAAAACCTCCCAAAGTGAATCTAATCTTAAAACTACAAGTTGTAAGTATTCTGAAATTGGGAAACATTTATTTTAAATGCAATCAGGTAGTGTTGCTTTTTACAGCATAATAAATATATGTATCAAAAAAAAAA\"\n",
- "find_all_aa_seqs(a,enst)"
+ "transcripts_filename = \"/home/annaldas/projects/result/ONECUT2/ONECUT2_seq.fa\"\n",
+ "transcripts = SeqIO.index(transcripts_filename, \"fasta\")\n",
+ "\n",
+ "gene = \"ONECUT2\"\n",
+ "\n",
+ "for transcript in transcripts:\n",
+ " seq = str(transcripts[transcript].seq).strip()\n",
+ " enst = str(transcripts[transcript].id).split(\"|\")[-1].strip()\n",
+ " protein = find_all_aa_seqs(seq,enst,gene)\n",
+ " transcript_name = str(transcripts[transcript].id)\n",
+ " transcript_name = str(transcripts[transcript].id)\n",
+ " transcript_filename = transcript_name.replace(\"|\",\"_\")\n",
+ " transcript_filename = transcript_filename.replace(\"_\",\"\")\n",
+ " print(transcript_name,transcript_filename,protein)\n",
+ " \n",
+ "#enst = \"enst\"\n",
+ "#a=\"TGGACAGCTCCCGCTCACCCAAACAGAAGACGTCGGCGCCGGAGCGGGCTCGGACATGGCGAGGCTGCGAGCCGGCCCGAGCGGCGGGGCCCGGTGATCCCTCCCTCCCTCCCCGTCCCCTCCCCTCTCCCGCACGCACGCCCCGTCCGCCCCCACCCCGCCCCCACCCCGGGCGAGCCCGCCCGCAGCCCGGGGCGCACACCCGCACGCGCACTCCTCTCCACTCACTCCCGCGCCCGCCCCCACTCCCGCAGCCGAGCCCCGCCACGCGCGCCTTGCCCGCCCGCCGGCCGCCCCCGCCGCCCCCGCCGCCCCCGGGCCCTGATGGACTGAATGAAGGCTGCCTACACCGCCTATCGATGCCTCACCAAAGACCTAGAAGGCTGCGCCATGAACCCGGAGCTGACAATGGAAAGTCTGGGCACTTTGCACGGGCCGGCCGGCGGCGGCAGTGGCGGGGGCGGCGGCGGGGGCGGCGGGGGCGGCGGCGGGGGCCCGGGCCATGAGCAGGAGCTGCTGGCCAGCCCCAGCCCCCACCACGCGGGCCGCGGCGCCGCTGGCTCGCTGCGGGGCCCTCCGCCGCCTCCAACCGCGCACCAGGAGCTGGGCACGGCGGCAGCGGCGGCAGCGGCGGCGTCGCGCTCGGCCATGGTCACCAGCATGGCCTCGATCCTGGACGGCGGCGACTACCGGCCCGAGCTCTCCATCCCGCTGCACCACGCCATGAGCATGTCCTGCGACTCGTCTCCGCCTGGCATGGGCATGAGCAACACCTACACCACGCTGACACCGCTCCAGCCGCTGCCACCCATCTCCACCGTGTCTGACAAGTTCCACCACCCTCACCCGCACCACCATCCGCACCACCACCACCACCACCACCACCAGCGCCTGTCCGGCAACGTCAGCGGCAGCTTCACCCTCATGCGCGACGAGCGCGGGCTCCCGGCCATGAACAACCTCTACAGTCCCTACAAGGAGATGCCCGGCATGAGCCAGAGCCTGTCCCCGCTGGCCGCCACGCCGCTGGGCAACGGGCTAGGCGGCCTCCACAACGCGCAGCAGAGTCTGCCCAACTACGGTCCGCCGGGCCACGACAAAATGCTCAGCCCCAACTTCGACGCGCACCACACTGCCATGCTGACCCGCGGTGAGCAACACCTGTCCCGCGGCCTGGGCACCCCACCTGCGGCCATGATGTCGCACCTGAACGGCCTGCACCACCCGGGCCACACTCAGTCTCACGGGCCGGTGCTGGCACCCAGTCGCGAGCGGCCACCCTCGTCCTCATCGGGCTCGCAGGTGGCCACGTCGGGCCAGCTGGAAGAAATCAACACCAAAGAGGTGGCCCAGCGCATCACAGCGGAGCTGAAGCGCTACAGTATCCCCCAGGCGATCTTTGCGCAGAGGGTGCTGTGCCGGTCTCAGGGGACTCTCTCCGACCTGCTCCGGAATCCAAAACCGTGGAGTAAACTCAAATCTGGCAGGGAGACCTTCCGCAGGATGTGGAAGTGGCTTCAGGAGCCCGAGTTCCAGCGCATGTCCGCCTTACGCCTGGCAGCGTGCAAACGCAAAGAGCAAGAACCAAACAAAGACAGGAACAATTCCCAGAAGAAGTCCCGCCTGGTGTTCACTGACCTCCAACGCCGAACACTCTTCGCCATCTTCAAGGAGAACAAACGCCCGTCAAAGGAGATGCAGATCACCATTTCCCAGCAGCTGGGCCTGGAGCTCACAACCGTCAGCAACTTCTTCATGAACGCCCGGCGCCGCAGCCTGGAGAAGTGGCAAGACGATCTGAGCACAGGGGGCTCCTCGTCCACCTCCAGCACGTGTACCAAAGCATGATGGAAGGACTCTCACTTGGGCACAAGTCACCTCCAAATGAGGACAACAGATACCAAAAGAAAACAAAGGAAAAAGACACCGGATTCCTAGCTGGGGCCCTTCACTGGTGATTTGAAAGCACAATTCTCTTGCAAAGAAACTTATATTCTAGCTGTAATCATAGGCCAGGTGTTCTTCTTTTGTTTTTAATGGCTATGGAGTCCAAGTGCAAGCTGAAAAATTAATCTCTTAGAACCAGACACTGTTCTCTGAGCATGCTAAGCATCCCAGAAACCCAAATGGGGCCTTCCTGGAGCGAGTTAATTCCAGTATGGTGTCAACCAAGCTCGGGATTGCTTAAAATATCATCCATCCCACTTCAGGTCCTGTCAGCTTCTTGCAGTCAGAGTTCCTATGAGTAACAATAGGAGTTTGGCCTATGTAAGGACTCTGAGTTTAGGCTTCCAAGATACAACAATAAGAGAAGAATCTAGCAACGAGAATGACCTCATTTGCTTTCCACATGCTTAGCCTCATTATACCATGTTATGTCCAAGTTCACAGCCACAACATCAGAATGGTAATTACTGAGCACAAGTTTTAAATATGGACGTTAAAAAAAAAAATCCAAGGACCTGTTTTTCCAACCCAGACATCTTTTCATTGAATGATTTAGAAAGCTTTAAGTTGATCCAGCTTACAATTTTTTTTTTCTTTACCTCCTGGAAATCTCATATGGTCTTGGATCCGTCAAAAAAACCAGTCAGTTCACTTGCGCTCAAAGTATCAAGCACAACAAAGATAAACAGAAGTGAGGAAGGTTCTGGGTTCACTACATCTGGATTTTCAAGACACCTATTGTGAAGTCATTAGGGAATTGATGAGAATATGGCTTCAAGCACATTTTGCAGTTTGCTACAAATTCTGTTGTACATAATGCAGACGCACACTCAGGAGGCCAATTTAACTGTTAACAGTGCATGGAGCGAATGCAGCATTTTAAAAGATCTAGGTTTTTTTAGGTCATTAATGTGTCCTTGGTTGATCAGTCATCTGGTCCCTCCTACTGTGTGTTATGACCACCACGTAATCCATTCTCGCTCTTTCTGATTTGGGGTTTTTCCTCATCCATCCCATTAGTAGGGATGTTTTCTGTGTTTTCTAGCAAGAAAAAAAAATCAATCAATCAAACCTGCATACATGTTACTCATGACTGTCATCTAGTCCTAAATCTCTTCTGTTGTTGAATCATCCTTGCAAAACAGCTGAATACATCTGGAGAAAACACAGCACACCAAAGAAGCAGAATACTGCAAACCAAAGACATTTATGACTTGTCATTTTCTAGCCTAAAAATACTGTGATTACTTTTAGAAATCAGAAAACCTCTGCAACTCCGAATGGCATTCAGCTCTTGCATTTGGCGCATCATCGGGCTGAGCGGACCAGCTACACCAAGGACATTAGCCAAGCCACCCAGAGGGGTGGCTTTGCCACACCAGTTGTCACCTTCCCATAGCAAGTGGAAGAGCGCCCACAGAACTCTGGGAGATTGCAAAGGTCACAATGTGCATATTTACCAGTGAATGGCCCCGGGTGGGGCCACGTGGGGGTGTTCAAAGCAAGCCAAACGCTGCAATCATTCTTTACAGACACTTGAGACTGACTTTTTTATGAATTACTTAGTCGAAACCAAAGAAACTTTTTCTGCACCTACTTCTGCAACAAACAAAACTGTCCCATTAAAATGAATAAATAAATCCGTAAATCAATGGAAATCACCACCAATAAGAAGGAAGCACGCCAGAAAATAAACGAAAACAAAAACAGGGAGACACACTGTGTTCAAACAGACCTCTTGGGACATTTTTTGGAAGCAGATTTTAAAGAAAGGGTTGAGACAAAGATAGAAATAAGGAAGAGCCTCAGTGGCTGCTGCTTCATTTGACAACTCACACGGTAATCTTAAAGCTGAAGATTGTCTTTAATTTGTGCCTATGCAGTTTTTCAAAAGAACACGGAACAGAGCAACAGAAACCTCAACAGCTACAATACCAAAGATGAGGATTTCTCACACCTTTTGTTTCAGTTCATTATCTCCTCTTGCCTGGCTAAAATACTAATAGCGCCATTGAACTGTATAAAGGTAATCAATTATGTTTCTCTGAGCAACAAAAGGAAAGGGCCATTTATTTGATTTTATTGTTTCATTTCAATTTTGTCTTATGGTTTTTTGCCCCAACATGGAATCTCTCAAAAGTTTCCATGGACTCCAAGTTTAAGATGTTGGGATATTGAACAGTTCTCTCTGCTCAGCAGAGGGTAGGGAATAACATTATCACTTGAATGTTCTTTGCTTAACCCTTAGACTTGGTTCCTTCTATGTTCAGAGTCTCATCATCAGGGGAAGGAAAGGGAGTGAGGGTCAGGGATAGGGGTCTTGGTGATGCATCCTCTCCCGAGCCACAGAACCAAAGAGTTTATAGAGGAATTTACAGCCTCGTTTTCATGTGATTGCTACATCCTAACAGGGCTTCATTTGGGGGTGGGGGGAAACATGTAAAAATAATTGCCAGTTTCTACTTTTCTATTAGCTTTTTAAAAATCAGCTGTAAAGTTGCATTTCTAAAGAAAGATATATATAATATATAAAATACATATATAGATCAACTTGACATTGGTGATAACCAAAATTATTGCTGTCCAAATTCATGTCTTGTTTTGGTCCAGTGCTTCATTTGCTAAGTATTCGGTTCAGAATTTTTCTCATTTCTCATGCCATTCCAGAGTTAATTTGCCACTGTGGATGATTTGAAGTATTCAGATCTCTATGGAAGTTTCTGGGACAGGTTTAAAGTCAAGATCAAGCATTTTAGCATTTAACCTGTTGATAAATGGATCCATGGTGTACATGAGTTTTATTTGTATTCGGAGTCATCTCTATTCTATCCCTCAGCCTCGATTAAGGTGGTGAGTGAAGTGCATCCAACAGACTCGGCCCAGAACTGGGTCCTGACAGTGGGGTGCTCATCTTCTGTAACTGTTGGGAAGGCTCGGTGGTCCATTTTCACCAGTTAAAGAATATGAGGCCAGCCCAGAAATCTGTTCTCCAGGAGCTGCCCTGTCCCATCTGGGTGTGCCAGACCCCCTCAGTGAGCAGGTCCACCAAAGGGACTTCTCACAGGGGAAGCCCAACTCCTGTTGCAATGGGTTGATAGATTTCCTCAGGGTGGTAATTACCAATTCGTATTTTGACAAGCCTATGTGCAACCACAGCTGGCACTGGGGTGGGCAGTGGTGTTGGGTGGGATGGGGGAGAGTGTCTCAATCCTGAAGAGAAAATATAAAGCAGGTTTTGGGGAGACTTCTGGAGTCCTGCCCCTAGAGAGCCCCATTGTTGTTCTTTGTGCCCCCTCCTCATTCCCCCTATGTGGGTCTCCCTATGCAGGAGCTGTGAGAGAATGTGACTCTCCACAATTTTTATAATTCATCCTTCCTAGGAGATTGTTCATTGGCTCTTCCCTTGTGTCCCTTTGTCCCTTGCTCATACTCCATGTTTCCTTTGTCAAAGGACTAAGAAAAGAGCATATTTCAGCAGAGGAGTGTTCCCATGTGGGTTGATTTCAACTTGGGTATTTCTAAAAGAGTCCTTGTGACATGTGTCCAGTGGAAATGGTTGCTCTTTTCCAGACTGGATTGAGGAATGGAGCCTGTTTGATTTGGTTAGTGATTCTTTGACATACTAATCTCAGCGTTTGGGTCTCCAGCATCCTCTGAAGATGTCTAGACTAGTAGAGGCTGCCTTTGTGACCTGACATTACAACATTGGTCAAACCAGTCCTCTGATAATCAGAAGAACATGTCATAATTGTTTAAAAAAAAAAAAAAGGCAAGAATTTCTCTCCAAGGAGCTTTAATAAATGTCTCATTCCAGATAATGTCATACCAGAGAAAAGTGCTTGCTTTTAGAAAATTATTTACATACATATATAAATATATATGTGTATCTATACAGTTATGTATCAAAATTTTAAGCCCTGCAGAATTTCAATTTGTTAGAAATCTAACAGAAAAAAATTTCTATATTGAAAGGTAATAGAATTTAACCCAGTGAGTTTACTCAAGGATTTTTAAATTTAAGTTAATAATTTCAGAGAAAATAACCATTTGGGTGTGGTTATAGTTTAGTATCCATTACCTCAATCCAAGGAAAATTCCAGGCATTCCTCAACCATCAGGAAAAGGTACAGTGTGAAGGAACAGTTCTCAGCCAAATTTCACATTCTTGAGGCAACAGAAATCAAAACACTCAGAGCCATTGAGTGGAAAAACAATTTACTTTATTCCTTTACACAAATAGGCTTGCATTGTTTTTGTTTTAATGTGATTTTGGTACTAGGGATATAATTATTTCATTCCAGGAAATAATAAAAAAAAACAGACAGAGCCAATACATTTCTTTTTTTAAAGGAAACAGCAACAACAATAAAAACTCAGCACCAATATTTAAAAGCTTTTCCAAAATGTAAAAGAAGTGTTTAGCTTGCACCATGCATAAAGGTGCAGGCTAGTTGAACCAGGAAGCATGGCACTTCCTCTGGAGAAATCCAGAAAGAGTTGCTTCTAAGCTCCCTTTTCCCCCTGCAGGCTCTTGGCAATTGTAGGCTTTAGCAAATCCAGAATAATTTTCAATTCAAGCTAAAATAAAATCAACATTTGGAATGTAAATCTGATACACACACACTTTTCTAAGTCAAACAACATATTTCAAAACCAAAAATAAATACCTTTTAGATAATCAGTTATTTTCTTTGTCTATACTGGGCACCCACCTACTAGTGCCAGTAAATTCAAGTTGAACAGATTTTTAAAATCACTATTATCTGGGTATGGGGGAAACTTCCCCACTTTTGAAAATGTTGGTAGAATTATAGGAATGTCTGTTTGATTATCATTACCAAAGTGTCATGACAGTATGCCTTTGTAGTGAACTCGGATTTTCAGGAGTTTGAATAGTTGGATATTTTAAAATCTAAGAAGAAAAGGCCTGTTTCCAATGTTGTTGAAGAATAATGAACTCTATTAAAAAGTGGAGAAAAAGATAATACATGTGGTCAAGGTTGACCACAAGGCCCAGGCACAACTACCTTGGCGATAATCTTCTAGATTCGTAACAGGTTAGAGCTGACTTTTTGTTTTTGTTGTTGCTGATGCTGTGTGATTCAGACTTCTCAGCCTAACCAGGAAGAGTAAGTGGAAATGGTAGATGAAGAAGGGGTAGAGCTGGTGTATCTATAACTTTCTGATATTTGTCTGCCAAACTTGATATATTAGTAATTTTTTTATCTTTAGCTAAGATCAAGTCACCCCTGAAACAACAGGAGATTCTAGTTTTAAAATAAGGCCACAAAAATCCTTACGGAATGAAGAATGGCACCCCAGTTGGTTGTATAAGTCTCATAAGATAATGATGTTGATTTTAAATATGGATGTCTCAATGCCTGTTTTCTATCAATGATTTGTTTGTTTCCAAGGTCGGGGAGGGAAAGAGGGGAGGGTTTATCTGTTTTAGAAAGTCTCAGAATACTTATAAAATACAGAAGTAGTTATTAAAATATATAGGACCTCACATAGGTAGATACAGAACTTACCATTGAGGCTGATGGGCTGTTGTGTGAATCACACAGGACCTTAAATGAGGCTCATTATTCTCACACACCAAAATGACTCTGACAGCCTGAAGCAGTTATTGCTAGAGCCCAAGCTTTCCTTGGAGGTTTTGGAGTTAGGTTGATTGGAAGTAACCAGCTAATACCTTTTCTAGTGGAGAAAAAGACATTGCTACCAGCTTGTTCATCCCATAGAAGTCTTCCACTCTGCTCCATTTTTAGCAGCAAGCATTTCATGTAGCATAAACCTTGGCAGATAAGTGTGCCTAAGGTTTATACAGTCTGTCCGCTTGGATGTATACAAATTTAGATACATATTTTAACATGTGTTCTCATAGATGACTTTATAACAACACACATTACCTATAGGTGTCTAGACTGTGTACATACAAGTGTGTACAGACAAGCTTCATACGTATATACTGTAATCCGTTACAACAAATAAATTTTAAATCATCGTTTAACATGTATGTGGTACTTCTACAGTGTACATTGTTTTCATTATTTATTGTAACATTGAAAACCACAGTGCAGGGAAAACAAAAGTATCCCAGCATCTTCATCCTGTACACTTGGAATTAATTTCATTTGGGCATATCCAAGATAAACTCAACTTTCAAGAAATCTTGTATATTATTTAATCATCTGTGTTAGGATGACACCTATGATTGATGACTTCGGTTGAATAGCTTTATTCTGGATTTTTCATAACTAAAGCTAAATCCAAAGACCTGAAAAAGGACAAAAAGAAAAAAAAAAAAAGAAA\"\n",
+ "#find_all_aa_seqs(a,enst,\"ONECUT2\")"
]
},
{
@@ -954,18 +791,25 @@
"execution_count": null,
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "test = determine_utrs(\"ONECUT2\")\n",
+ "for i in test:\n",
+ " for j in test[i]:\n",
+ " print(i,find_utrs(a,j), j)"
+ ]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
- "source": []
+ "source": [
+ "len(\"MALNGAEVDDFSWEPPTEAETKVLQARRERQDRISRLMGDYLLRGYRMLGETCADCGTILLQDKQRKIYCVACQELDSDVDKDNPALRDVVPQPLPF\") *3"
+ ]
},
{
"cell_type": "code",
- "execution_count": 18,
+ "execution_count": null,
"metadata": {},
"outputs": [],
"source": [
@@ -1010,25 +854,9 @@
},
{
"cell_type": "code",
- "execution_count": 20,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "{'TCONS_00010063|ENST00000533115': {'IPR039499'},\n",
- " 'TCONS_00010061|TCONS_00010060': {'IPR009563'},\n",
- " 'TCONS_00010064|ENST00000533115': {'IPR009563'},\n",
- " 'TCONS_00011857|ENST00000531405': {'IPR009563'},\n",
- " 'TCONS_00010062|ENST00000533115': {'IPR009563'},\n",
- " 'TCONS_00010060|ENST00000533115': {'IPR009563'}}"
- ]
- },
- "execution_count": 20,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"domains"
]
diff --git a/test/list.txt b/test/list.txt
index a6957de..5e478ac 100644
--- a/test/list.txt
+++ b/test/list.txt
@@ -1,38 +1,27 @@
-BRD4
-BRD3
-BRD2
-PAF1
-CTR9
-CDC73
-LEO1
-RTF1
-WDR61
-SPT5
-SPT4
-SPT6
-TCEA1
-TCEA2
-TCEA3
-TCEANC
-TCEANC2
-CDK9
-TRIM28
-SUPT16H
-SSRP1
-ELF1
-CDK12
-SUPT16H
-SSRP1
-ELL2
-AFF4
-SKI
-CCNT1
-NELFA
-NELFB
-NELFC
-NELFD
-NELFE
-TCEAL
-SNUPN
-MYC
-MLLT1
\ No newline at end of file
+SMARCC2
+SMARCB1
+SMARCE1
+SMARCD1
+SMARCD2
+SMARCD3
+BRD7
+SMARCA4
+SMARCA2
+ARID1A
+ARID1B
+ARID2
+PBRM1
+ACTL6A
+ACTL6B
+PHF10
+DPF1
+DPF2
+DPF3
+BCL7B
+BCL7A
+BCL7C
+BRD9
+BCL7C
+SS18
+SS1BL1
+GLTSCR1L
diff --git a/translation_protein.py b/translation_protein.py
index 1dabda4..a754d89 100644
--- a/translation_protein.py
+++ b/translation_protein.py
@@ -1,11 +1,7 @@
from Bio import SeqIO
import os
-def translate(seq,orf):
- seq = seq.upper()
- seq = seq.replace("\n","")
-
- table = {
+codon_table = {
'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M',
'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K',
@@ -22,80 +18,133 @@ def translate(seq,orf):
'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L',
'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_',
'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W',
- }
+ }
- protein = ""
- exon = False
- translating = True
- i = orf
+def determine_utrs(gene):
+ utr_file = open(snakemake.input[0],"r")
+ utr_lines = utr_file.readlines()
+ utr_file.close()
+ gene_utr = dict()
+
+ for line in utr_lines:
+ if (line.startswith(">")):
+ trans_id = line[1:].strip()
+ if (trans_id not in gene_utr):
+ gene_utr[trans_id] = []
+ else:
+ gene_utr[trans_id].append(line.strip())
+ return gene_utr
- while (translating):
- codon = seq[i:i+3]
+def score(seq,start):
+ kozak = {
+ "A":[0.25,0.61,0.27,0.15,1.00,0.00,0.00,0.23],
+ "C":[0.53,0.02,0.49,0.55,0.00,0.00,0.00,0.16],
+ "G":[0.15,0.36,0.13,0.21,0.00,0.00,1.00,0.46],
+ "T":[0.07,0.01,0.11,0.09,0.00,1.00,0.00,0.15]
+ }
+
+ score = 1.0
+ for i in range(start,len(seq)):
+ score *= kozak[seq[i]][i]
+ return score
- try: table[codon]
- except: break
-
- if (table[codon] == "M"):
- exon = True
- if (exon):
- if (table[codon] == "_"):
- exon = False
+def translate(seq, i, utr_regions):
+ translating = True
+ aa = ""
+
+ in_utr = False
+ for utr in utr_regions:
+ start,stop = utr
+ if ((start < i) and (i < stop)):
+ in_utr = True
+
+ while(translating):
+ if ((len(seq) < 3) or (in_utr)):
+ translating = False
+ aa = ""
+ else:
+ codon = seq[0:3]
+ if (codon_table[codon] == "_"):
translating = False
else:
- protein += table[codon]
- i += 3
- else:
+ aa += codon_table[codon]
+ seq = seq[3:]
i += 3
-
- return protein
+ return aa,i
+def find_utrs(seq,utr):
+ pos = seq.find(utr)
+ if (pos == -1):
+ if (len(utr) > 20):
+ for i in range(len(utr) - 1,len(utr)*5//10 - 1,-1):
+ pos = seq.find(utr[:i])
+ return pos
+def translate_aa_seq(seq,enst,gene_utrs):
+ utr_regions = []
+ for utr in gene_utrs[enst]:
+ pos = find_utrs(seq,utr)
+ if (pos != -1):
+ utr_regions.append([pos,pos + len(utr)])
+
+ longest_aa_seq = "M"
+ longest_aa_seq_sc = 0
+ longest_aa_seq_sc_end = 0
+ for i in range(len(seq)):
+ if (seq[i:i+3] == "ATG"):
+ sc = score(seq[i-4:i+4],0)
+ aa,end = translate(seq[i:], i, utr_regions)
+ #print(i,seq[i-4:i+4],aa,sc, end)
+ if ((len(aa) > 20) and (sc > longest_aa_seq_sc) and (i > longest_aa_seq_sc_end)):
+ longest_aa_seq = aa
+ longest_aa_seq_sc = sc
+ longest_aa_seq_sc_end = end
+ return (longest_aa_seq,longest_aa_seq_sc)
-transcripts_filename = snakemake.input[0]
+
+
+def translate_aa_seq_length(seq,enst):
+ utr_regions = []
+
+ longest_aa_seq = "M"
+ for i in range(len(seq)):
+ if (seq[i:i+3] == "ATG"):
+ aa,end = translate(seq[i:], i, utr_regions)
+ #print(i,seq[i-4:i+4],aa, end)
+ if (len(aa) > len(longest_aa_seq)):
+ longest_aa_seq = aa
+ return longest_aa_seq
+
+def find_all_aa_seqs(seq,enst,gene):
+ gene_utrs = determine_utrs(gene)
+
+ longest_aa_seq = translate_aa_seq_length(seq,enst)
+ if gene in gene_utrs:
+ for utr in gene_utrs[gene]:
+ if (find_utrs(seq,utr) != -1):
+ longest_aa_seq,longest_aa_seq_sc = translate_aa_seq(seq,enst,gene_utrs)
+
+ return longest_aa_seq
+
+
+transcripts_filename = snakemake.input[1]
transcripts = SeqIO.index(transcripts_filename, "fasta")
output = []
-gene = snakemake.input[0].split("/")[5]
-os.mkdir("/home/annaldas/projects/result/%s/transcripts" %(gene))
+gene = snakemake.params[0]
+os.mkdir("/project/owlmayerTemporary/Sid/isoform_analysis/result/%s/transcripts" %(gene))
for transcript in transcripts:
- protein = translate(str(transcripts[transcript].seq),0)
- if (protein != ""):
- transcript_name = str(transcripts[transcript].id) + "_1"
- transcript_filename = transcript_name.replace("|","_")
- transcript_filename = transcript_filename.replace("_","")
- transcript_filename_path = "/home/annaldas/projects/result/%s/transcripts/%s_map_protein.fa" %(gene,transcript_filename)
- #os.mkdir("/home/annaldas/projects/result/%s/transcripts/%s" %(gene,transcript_filename))
- transcript_file = open(transcript_filename_path, "w+")
- transcript_file.write(">" + transcript_name + "\n" + protein)
- transcript_file.close()
-
- protein = translate(str(transcripts[transcript].seq),1)
- if (protein != ""):
- transcript_name = str(transcripts[transcript].id) + "_2"
- transcript_filename = transcript_name.replace("|","_")
- transcript_filename = transcript_filename.replace("_","")
- transcript_filename_path = "/home/annaldas/projects/result/%s/transcripts/%s_map_protein.fa" %(gene,transcript_filename)
- #os.mkdir("/home/annaldas/projects/result/%s/transcripts/%s" %(gene,transcript_filename))
- transcript_file = open(transcript_filename_path, "w+")
- transcript_file.write(">" + transcript_name + "\n" + protein)
- transcript_file.close()
-
- protein = translate(str(transcripts[transcript].seq),2)
- if (protein != ""):
- transcript_name = str(transcripts[transcript].id) + "_3"
- transcript_filename = transcript_name.replace("|","_")
- transcript_filename = transcript_filename.replace("_","")
- transcript_filename_path = "/home/annaldas/projects/result/%s/transcripts/%s_map_protein.fa" %(gene,transcript_filename)
- #os.mkdir("/home/annaldas/projects/result/%s/transcripts/%s" %(gene,transcript_filename))
- transcript_file = open(transcript_filename_path, "w+")
- transcript_file.write(">" + transcript_name + "\n" + protein)
- transcript_file.close()
+ seq = str(transcripts[transcript].seq).strip()
+ enst = str(transcripts[transcript].id).split("|")[-1].strip()
+ protein = find_all_aa_seqs(seq,enst,gene)
-#output_filename = snakemake.output[0]
-#output_file = open(output_filename,"w+")
-#output_file.write("\n".join(output))
-#output_file.close()
-
-
\ No newline at end of file
+ transcript_name = str(transcripts[transcript].id)
+ transcript_filename = transcript_name.replace("|","_")
+ transcript_filename = transcript_filename.replace("_","")
+ transcript_filename_path = "/project/owlmayerTemporary/Sid/isoform_analysis/result/%s/transcripts/%s_map_protein.fa" %(gene,transcript_filename)
+ transcript_file = open(transcript_filename_path, "w+")
+ transcript_file.write(">" + transcript_name + "\n" + protein + "\n")
+ transcript_file.close()
+