diff --git a/Snakefile b/Snakefile
index 3678212..6b6bd58 100644
--- a/Snakefile
+++ b/Snakefile
@@ -10,8 +10,8 @@ Transcripts = config["polished_reads"]
 
 rule all:
     input:
-        expand("/home/annaldas/projects/result/{gene}/{gene}_map_protein_analysis.txt", gene = GENES),
-        expand("/home/annaldas/projects/result/{gene}/{gene}_blastx_protein_analysis.txt", gene = GENES)
+        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)
 
 rule gene_transcript:
@@ -19,8 +19,8 @@ rule gene_transcript:
         NanoporeGTF,
         Transcripts
     output:
-        "/home/annaldas/projects/result/{gene}/{gene}_seq.fa",
-        "/home/annaldas/projects/result/{gene}/{gene}_sashimi.sh"
+        "/home/annaldas/projects/result/{gene}/{gene}_seq.fa"#,
+        #"/home/annaldas/projects/result/{gene}/{gene}_sashimi.sh"
     params:
         gene = "{gene}"
     script:
@@ -75,41 +75,119 @@ rule transcript_filter_utr:
     script:
         "filter_utr.py"
 
-rule mapping:
+checkpoint mapping:
     input:
         "/home/annaldas/projects/result/{gene}/{gene}_seq_filt.fa"
     output:
-        "/home/annaldas/projects/result/{gene}/{gene}_map_protein.fa"
+        directory("/home/annaldas/projects/result/{gene}/transcripts") #/{transcript}/{transcript}_map_protein.fa"
+    params:
+        gene = "{gene}"
     script:
         "translation_protein.py"
         
+rule iupred2a_analysis:
+    input:
+        "/home/annaldas/projects/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"
+    script:
+        "iupred2a_analysis.py"
+        
 rule interpro_scan:
     input:
-        "/home/annaldas/projects/result/{gene}/{gene}_{type}_protein.fa"
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa"
     output:
-        "/home/annaldas/projects/result/{gene}/{gene}_{type}.gff3"
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map.gff3"
     params:
-        db = "Pfam,ProDom,Gene3D,CDD,Coils,MobiDBLite"
+        db = "Pfam,ProDom,Gene3D,CDD,Coils,MobiDBLite,SMART"
     shell:
         "sh /home/annaldas/my_interproscan/interproscan-5.38-76.0/interproscan.sh -i {input} -o {output} -f GFF3 -appl {params.db} -dra"
         
-rule protein_domain_analysis:
+rule brewery_analysis:
     input:
-        "/home/annaldas/projects/result/{gene}/{gene}_{type}.gff3"
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa"
     output:
-        "/home/annaldas/projects/result/{gene}/{gene}_{type}_protein_analysis.txt"
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa.ss3"
+        #"/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa.ss8"
     params:
-        gene = "{gene}"
+        brewery = config["brewery"]
+    shell:
+        "python3 {params.brewery} -i {input} --cpu 32 --noTA --noSA --noCD" 
+
+rule functional_site_analysis:
+    input:
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein.fa"
+    output:
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_sites.txt"
+    params:
+        ps_scan = config["prosite_scan"],
+        prosite_dat = config["prosite_dat"]
+    shell:
+        "perl {params.ps_scan} -d {params.prosite_dat} {input} > {output}"
+
+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"
+    output:
+        "/home/annaldas/projects/result/{gene}/transcripts/{transcript}_map_protein_analysis.txt"
     script:
-        "interproscan_analysis.py"
+        "transcript_analysis.py"
         
-rule sashimi_plot:
+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",
+           gene=wildcards.gene,
+           transcript=glob_wildcards(os.path.join(checkpoint_output,"{transcript}_map_protein.fa")).transcript)
+
+rule aggregate:
     input:
-        sashimi_sh = "/home/annaldas/projects/result/{gene}/{gene}_sashimi.sh",
-        sashimi_py = config["sashimi"],
-        bams = config["input_bams"],
-        gtf = NanoporeGTF
+        aggregate_input
     output:
-        "/home/annaldas/projects/result/{gene}/{gene}_sashimi.pdf"
+        "/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_analysis.txt"
+    params:
+        gene = "{gene}"
     shell:
-        "sh {input.sashimi_sh} {input.sashimi_py} {input.bams} {input.gtf} {output}"
\ No newline at end of file
+        "cat {input} > {output}"
+        
+#rule filter_transcripts:
+#    input:
+#        "/home/annaldas/projects/result/{gene}/{gene}_transcripts_analysis.txt"
+#    output:
+#        "/home/annaldas/projects/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"
+    output:
+        "/home/annaldas/projects/result/{gene}/{gene}_transcripts_filtered_coding_potential_analysis.txt"
+    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"
+#    output:
+#        "/home/annaldas/projects/result/{gene}/{gene}_map_protein_analysis.txt"
+#    params:
+#        gene = "{gene}"
+#    script:
+#        "interproscan_analysis.py"
+        
+#rule sashimi_plot:
+#    input:
+#        sashimi_sh = "/home/annaldas/projects/result/{gene}/{gene}_sashimi.sh",
+#        sashimi_py = config["sashimi"],
+#        bams = config["input_bams"],
+#        gtf = NanoporeGTF
+#    output:
+#        "/home/annaldas/projects/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 be78531..ef2b0f8 100644
--- a/gene_transcripts.py
+++ b/gene_transcripts.py
@@ -73,12 +73,12 @@
 
 # Create sashmimi sh
 
-output_filename = snakemake.output[1]
-output_file = open(output_filename,"w+")
-
-chrm,start,stop = gene_pos[gene][0],gene_pos[gene][1],gene_pos[gene][2]
-binbash = "#!/bin/bash"
-sashimi = "python $1 -b $2 -c %s:%d-%d -g $3 -M 10 -C 3 -O 3 --shrink --alpha 1 --base-size=20 --ann-height=5 --height=7 --width=18 -S both -o $4" %(chrm,start,stop)
-output_file.write("\n".join([binbash,sashimi]))
-output_file.close()
+#output_filename = snakemake.output[1]
+#output_file = open(output_filename,"w+")
+
+#chrm,start,stop = gene_pos[gene][0],gene_pos[gene][1],gene_pos[gene][2]
+#binbash = "#!/bin/bash"
+#sashimi = "python $1 -b $2 -c %s:%d-%d -g $3 -M 10 -C 3 -O 3 --shrink --alpha 1 --base-size=20 --ann-height=5 --height=7 --width=18 -S both -o $4" %(chrm,start,stop)
+#output_file.write("\n".join([binbash,sashimi]))
+#output_file.close()
 
diff --git a/genes.tab b/genes.tab
index 7dc3bf5..ba1c398 100644
--- a/genes.tab
+++ b/genes.tab
@@ -1,15 +1,2 @@
 gene_symbol
-APP
-ABI2
-DNMBP
-SEPTIN8
-EPB41L5
-SEPTIN6
-TFDP2
-ERBB2
-RPS24
-ZNRD2
-COX11
-ERGIC3
-PFN2
-NKAIN4
\ No newline at end of file
+RPS24
\ No newline at end of file
diff --git a/interproscan_analysis.py b/interproscan_analysis.py
index e69de29..62037c5 100644
--- a/interproscan_analysis.py
+++ b/interproscan_analysis.py
@@ -0,0 +1,59 @@
+filename = snakemake.input[0]
+file = open(filename, "r")
+lines = file.readlines()
+file.close()
+
+class transcript:
+    def __init__(self, tcons, idr, ips, ss8):
+        self.tcons = tcons
+        self.idr = idr
+        self.ips = ips
+        self.ss8 = ss8
+        self.pss = pss
+
+transcripts = dict()
+
+idr_lines = []
+ips_lines = []
+ss8_lines = []
+pss_lines = []
+
+for line in lines:
+    if (line.startswith(">")):
+        if (len(ips_lines) > 0):
+            transcripts[tcons] = transcript(tcons, idr, ips, ss8)
+            
+        new = True
+        idr_lines = []
+        ips_lines = []
+        ss8_lines = []
+        pss_lines = []
+        idr = False
+        ips = False
+        ss8 = False
+        pss = False
+        tcons = line[1:].strip().split("|")[0]    
+        
+        
+    if (line.startswith("#####IUPred2A Analysis")):
+        idr = True
+    elif (line.startswith("#####InterProScan")):
+        ips = True
+        idr = False
+    elif (line.startswith("#####BrewerySS8 Analysis")):
+        ss8 = True
+        ips = False
+    
+    if (idr):
+        idr_lines.append(line.strip())
+    elif (ips):
+        ips_lines.append(line.strip())
+    elif (ss8):
+        ss8_lines.append(line.strip())
+        
+transcripts[tcons] = transcript(tcons, idr, ips, ss8)
+
+
+
+
+print(transcripts)
\ No newline at end of file
diff --git a/isoform_transcripts.ipynb b/isoform_transcripts.ipynb
index d574150..0c4f65c 100644
--- a/isoform_transcripts.ipynb
+++ b/isoform_transcripts.ipynb
@@ -23,7 +23,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": 25,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -34,7 +34,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 38,
+   "execution_count": 24,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,14 +71,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 51,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['4e6fca82-c640-4aac-be00-57223afed52e|41',\n",
+       " '0807443e-5f7f-4b1b-b59f-b6a737ad89a9|16']"
+      ]
+     },
+     "execution_count": 51,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "gene_oID[\"MLLT1\"]"
+   ]
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 26,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -95,7 +109,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -139,23 +153,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": 27,
    "metadata": {},
    "outputs": [
     {
      "ename": "KeyError",
-     "evalue": "'cc2e8b66-6da7-4245-9544-c06d33b50252'",
+     "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-41-bb4ce5b62c91>\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\"cc2e8b66-6da7-4245-9544-c06d33b50252\"\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: 'cc2e8b66-6da7-4245-9544-c06d33b50252'"
+      "\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'"
      ]
     }
    ],
    "source": [
-    "oID_tID[\"cc2e8b66-6da7-4245-9544-c06d33b50252\"]"
+    "oID_tID[\"142e462f-f586-42fc-97b9-b2e3bfa1fd0d\"]"
    ]
   },
   {
@@ -441,11 +455,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 222,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
-    "afilename = \"/home/annaldas/projects/nanopore-transcriptome-analysis/ReferenceData/gencode.v32.primary_assembly.annotation.gtf\"\n",
+    "afilename = \"/project/owlmayerTemporary/Sid/nanopore-analysis/ReferenceData/gencode.v32.primary_assembly.annotation.gtf\"\n",
     "afile = open(afilename,\"r\")\n",
     "afile_lines = afile.readlines()\n",
     "afile.close()"
@@ -453,18 +467,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 298,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "['gene' 'transcript' 'exon' 'CDS' 'start_codon' 'stop_codon' 'UTR'\n",
-      " 'Selenocysteine']\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "output = []\n",
     "for line in afile_lines:\n",
@@ -472,8 +477,8 @@
     "        output.append(line.strip().split(\"\\t\"))\n",
     "pd_aline = pd.DataFrame(output,columns=[\"chr\",\"source\",\"type\",\"start\",\"stop\",\"a\",\"b\",\"c\",\"info\"])\n",
     "pd_aline = pd_aline.astype({'start': 'int32', \"stop\":\"int32\"})\n",
-    "print(pd_aline[\"type\"].unique())\n",
-    "#pd_aline = pd_aline[pd_aline[\"type\"] == \"UTR\"]\n"
+    "#print(pd_aline[\"type\"].unique())\n",
+    "pd_aline = pd_aline[pd_aline[\"type\"] == \"UTR\"]\n"
    ]
   },
   {
@@ -507,18 +512,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 224,
+   "execution_count": 6,
    "metadata": {
     "scrolled": true
    },
    "outputs": [],
    "source": [
-    "pd_aline.to_csv(path_or_buf = \"/home/annaldas/projects/nanopore-transcriptome-analysis/df_utr_regions.csv\",index = False)"
+    "pd_aline.to_csv(path_or_buf = \"/project/owlmayerTemporary/Sid/nanopore-analysis/ReferenceData/df_utr_regions.csv\",index = False)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 15,
    "metadata": {
     "scrolled": true
    },
@@ -527,22 +532,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "chr11\t65570460\t65570695\tENST00000531405\n",
-      "chr11\t65571732\t65571888\tENST00000531405\n",
-      "chr11\t65570477\t65570491\tENST00000309328\n",
-      "chr11\t65571732\t65571888\tENST00000309328\n",
-      "chr11\t65570485\t65570695\tENST00000527920\n",
-      "chr11\t65572478\t65572892\tENST00000527920\n",
-      "chr11\t65570487\t65570491\tENST00000526877\n",
-      "chr11\t65571394\t65571858\tENST00000526877\n",
-      "chr11\t65571732\t65571779\tENST00000533115\n",
-      "chr11\t65572443\t65572892\tENST00000533115\n",
-      "chr11\t65573524\t65573942\tENST00000526433\n"
+      "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"
      ]
     }
    ],
    "source": [
-    "df_utr_regions = pd.read_csv(\"/home/annaldas/projects/nanopore-transcriptome-analysis/df_utr_regions.csv\")\n",
+    "df_utr_regions = pd.read_csv(\"/project/owlmayerTemporary/Sid/nanopore-analysis/ReferenceData/df_utr_regions.csv\")\n",
     "\n",
     "info = list(df_utr_regions[\"info\"])\n",
     "chrms = list(df_utr_regions[\"chr\"])\n",
@@ -556,18 +560,18 @@
     "        gene = line[3].split(\" \")[-1][1:-1]\n",
     "        \n",
     "        \n",
-    "        if (gene == \"ZNRD2\"):\n",
+    "        if (gene == \"EBF2\"):\n",
     "            print(chrms[ann] + \"\\t\" + str(start[ann]) + \"\\t\" + str(stop[ann]) + \"\\t\" + transID)\n",
     "        "
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 32,
    "metadata": {},
    "outputs": [],
    "source": [
-    "bedfastafile = open(\"/home/annaldas/projects/result/ZNRD2/ZNRD2_utr_regions.fa\")\n",
+    "bedfastafile = open(\"/home/annaldas/projects/result/RPS24/RPS24_utr_regions.fa\")\n",
     "bedfastalines = bedfastafile.readlines()\n",
     "bedfastafile.close()\n",
     "trans_utr = dict()\n",
@@ -579,31 +583,71 @@
     "    else:\n",
     "        trans_utr[trans_id].append(line.strip())\n",
     "\n",
-    "transcript_id = \"ENST00000533115\"\n",
-    "s = '''GGTGACAACGGCAACATGGCCCTGAACGGAGCTGGTGAGGACCTGGGCGGCAGGGGTTTGTGGCTGTGAGGTACGGGAGGCAGCCCACTCCGGCAAGACCCCCAGTCCCTATGCCTCTCTTCCCCAGAAGTCGACGACTTCTCCTGGGAGCCCCCGACTGAGGCGGAGACGAAGACGATCCTCCTCCAAGACAAACAGCGGAAAATCTACTGCGTGGCTTGTCAGGAACTCGACTCAGACGTGGATAAAGATAATCCCGCTCTGAATGCCCAGGCTGCCCTCTCCCAAGCTCGGGAGCACCAGCTGGCCTCAGCCTCAGAGCTCCCCCTGGGCTCTCGACCTGCGCCCCAGCCCCCAGTACCTCGTCCGGAGCACTGTGAGGGAGCTGCAGCAGGACTCAAGGCAGCCCAGGGGCCACCTGCTCCTGCTGTGCCTCCAAATACAGATGTCATGGCCTGCACACAGACAGCCCTCTTGCAGAAGCTGACCTGGGCCTCTGCTGAACTGGGCTCTAGCACCTCCCTGGAGACTAGCATCCAGCTGTGTGGCCTTATCCGCGCATGTGCGGAGGCCCTGCGCAGCCTGCAGCAGCTACAGCACTAAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAA'''"
+    "transcript_id = \"ENST00000372360\"\n",
+    "s = '''CTCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATCATGAACGACACCGTAACTATCCGCACTAGAAAGTTCATGACCAACCGACTACTTCAGAGGAAACAAATGGTCATTGATGTCCTTCACCCCGGGAAGGCGACAGTGCCTAAGACAGAAATTCGGGAAAAACTAGCCAAAATGTACAAGACCACACCGGATGTCATCTTTGTATTTGGATTCAGAACTCATTTTGGTGGTGGCAAGACAACTGGCTTTGGCATGATTTATGATTCCCTGGATTATGCAAAGAAAAATGAACCCAAACATAGACTTGCAAGACATGGCCTGTATGAGAAGAAAAAGACCTCAAGAAAGCAACGAAAGGAACGCAAGAACAGAATGAAGAAAGTCAGGGGGACTGCAAAGGCCAATGTTGGTGCTGGCAAAAAGTGAGCTGGAGATTGGATCACAGCCGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAAC'''"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
+   "execution_count": 33,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "1 TCTTTTCCTCCTTGGCTGTCTGAAGATAGATCGCCATC\n",
+      "392 GAGCTGGAGATTGGATCACAG\n",
+      "-1 CGAAGGAGTAAAGGTGCTGCAATGATGTTAGCTGTGGCCACTGTGGATTTTTCGCAAGAACATTAATAAACTAAAAACTTCATGTGTCTGGTTGTTTGAAA\n"
+     ]
+    }
+   ],
+   "source": [
+    "if transcript_id in trans_utr:\n",
+    "    seq = s\n",
+    "    for utr in trans_utr[transcript_id]:\n",
+    "        pos = seq.find(utr)\n",
+    "        print(pos, utr)\n",
+    "        if (pos != -1):\n",
+    "            seq = seq[:pos] + seq[pos + len(utr):]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 30,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "-1 TTCCTGTGAGCCCGGCGGTGACAACGGCAACATGGCCCTGAACGGAGCTGGTGAGGACCTGGGCGGCAGGGGTTTGTGGCTGTGAGGTACGGGAGGCAGCCCACTCCGGCAAGACCCCCAGTCCCTATGCCTCTCTTCCCCAGAAGTCGACGACTTCTCCTGGGAGCCCCCGACTGAGGCGGAGACGAAGGTGCTGCAGGCGCGACGGGAGCGGCAAGATCGCATCTCCCGGCTC\n",
-      "-1 AAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAAACAGCTGTTCCTCTGTGTGGTTTGTTTTTTTCCTGGTTCCAAGTGTGCATGCCAGCCCCAGCTCCACTCACCTTTTTCCAGCTTTTGGCCTCTTCACCTCTCCACTCTGCTCTCCTTGACGCC\n",
-      "1 GTGACAACGGCAAC\n",
-      "-1 AAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAAACAGCTGTTCCTCTGTGTGGTTTGTTTTTTTCCTGGTTCCAAGTGTGCATGCCAGCCCCAGCTCCACTCACCTTTTTCCAGCTTTTGGCCTCTTCACCTCTCCACTCTGCTCTCCTTGACGCC\n",
-      "-1 GGCAACATGGCCCTGAACGGAGCTGGTGAGGACCTGGGCGGCAGGGGTTTGTGGCTGTGAGGTACGGGAGGCAGCCCACTCCGGCAAGACCCCCAGTCCCTATGCCTCTCTTCCCCAGAAGTCGACGACTTCTCCTGGGAGCCCCCGACTGAGGCGGAGACGAAGGTGCTGCAGGCGCGACGGGAGCGGCAAGATCGCATCTCCCGGCTC\n",
-      "-1 AAGAGAGGCCCGGCCCATCCAGAGGGGGTGGGGCAGAGGCGGAGTCTGAGGAGCTGGGGAAGGAACAAAGCGAGGCCTGCGGGCGGCGGCTGGGCTCCGGCGGGGCCGCGGGGTGCGGGGCCTGCGGGCGGCGGCCCGGGCGGAGCGTTGGAGGGAAGGAGGTGGCATCGCCGTCCGCGCCGGCCCCGGCCATGAACGGGCTGCCCTCGGCAGAGGCGCCGGGCGGGGCGGGCTGCGCTTTGGCCGGGCTCCCACCGCTGCCGCGCGGCCTCAGCGGCCTCCTTAATGCGAGCGGGGGCTCGTGGCGGGAGCTGGAGCGCGTCTACAGCCAGCGCAGCCGCATCCACGACGAGCTGAGCCGCGCCGCCCGCGCCCCGGACGGGCCCCGCCACGCCGCCGGCGCCGCCAACGCGG\n",
-      "5 CAAC\n",
-      "-1 GAATGCCCAGGCTGCCCTCTCCCAAGCTCGGGAGCACCAGCTGGCCTCAGCCTCAGAGCTCCCCCTGGGCTCTCGACCTGCGCCCCAGCCCCCAGTACCTCGTCCGGAGCACTGTGAGGGAGCTGCAGCAGGACTCAAGGCAGCCCAGGGGCCACCTGCTCCTGCTGTGCCTCCAAATACAGATGTCATGGCCTGCACACAGACAGCCCTCTTGCAGAAGCTGACCTGGGCCTCTGCTGAACTGGGCTCTAGCACCTCCCTGGAGACTAGCATCCAGCTGTGTGGCCTTATCCGCGCATGTGCGGAGGCCCTGCGCAGCCTGCAGCAGCTACAGCACTAAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAAACAGCTGTTCCTCTGTGTGGTTTGTTTTTTTCCTGGTTCCAAGTGTGCATGCCAGCCCCAGCTCCACTCACCTTTTTCCAGCTTTTGGCCTCT\n",
-      "-1 AAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAAACAGCTGTTCCTCT\n",
-      "-1 TTTGCGCGACGTGGTCCCACAACCGTTGCCTTTTTAAGAGAGGCCCGGCCCATCCAGAGGGGGTGGGGCAGAGGCGGAGTCTGAGGAGCTGGGGAAGGAACAAAGCGAGGCCTGCGGGCGGCGGCTGGGCTCCGGCGGGGCCGCGGGGTGCGGGGCCTGCGGGCGGCGGCCCGGGCGGAGCGTTGGAGGGAAGGAGGTGGCATCGCCGTCCGCGCCGGCCCCGGCCATGAACGGGCTGCCCTCGGCAGAGGCGCCGGGCGGGGCGGGCTGCGCTTTGGCCGGGCTCCCACCGCTGCCGCGCGGCCTCAGCGGCCTCCTTAATGCGAGCGGGGGCTCGTGGCGGGAGCTGGAGCGCGTCTACAGCCAGCGCAGCCGCATCCACGACGAGCTGAGCCGCGCCGCCCGCGCCCCGGACGGGCCCCGCCACGCCGCCGGCGCCGCCAACGCGG\n",
-      "ENST00000533115 2 ['AAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAAACAGCTGTTCCTCT', 'TTTGCGCGACGTGGTCCCACAACCGTTGCCTTTTTAAGAGAGGCCCGGCCCATCCAGAGGGGGTGGGGCAGAGGCGGAGTCTGAGGAGCTGGGGAAGGAACAAAGCGAGGCCTGCGGGCGGCGGCTGGGCTCCGGCGGGGCCGCGGGGTGCGGGGCCTGCGGGCGGCGGCCCGGGCGGAGCGTTGGAGGGAAGGAGGTGGCATCGCCGTCCGCGCCGGCCCCGGCCATGAACGGGCTGCCCTCGGCAGAGGCGCCGGGCGGGGCGGGCTGCGCTTTGGCCGGGCTCCCACCGCTGCCGCGCGGCCTCAGCGGCCTCCTTAATGCGAGCGGGGGCTCGTGGCGGGAGCTGGAGCGCGTCTACAGCCAGCGCAGCCGCATCCACGACGAGCTGAGCCGCGCCGCCCGCGCCCCGGACGGGCCCCGCCACGCCGCCGGCGCCGCCAACGCGG']\n",
-      "-1 GACGACGAGGAGCCTCCCGATGCCAGCCTGCCTCCTGACCCGCCACCCCTTACTGTGCCCCAGACGCACAATGCCCGTGACCAGTGGCTGCAGGATGCCTTCCACATCAGCCTCTGAAGGGCTGGGGGGCAGGGGGCATGCACCCATGCAAAAGGCTCAGAAACTCCCCCTCCGGCAAGCCCTCAGACTTCGGAGCCTGCGCCTTCCCCCCTACCGCCTCACCTCACAGGAGGGCCAGGCATGTATTCCTCAGAGGCGAAACTGCCAAACTCTTTCTCCTGTCTTGGGTTGGCTGGCACTGGGGCGGGCATCTAGGGTACAGCCTCTGCTCATGGCACTGGGCCTCCAGTTCTTCCACATGTGTGCACCCCCAGCTTGGCCAACCCTCAGCCTTGCGGTGGGGCCCGAAGCATCTTCC\n"
+      "-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"
      ]
     }
    ],
@@ -615,14 +659,13 @@
     "        print(pos, utr)\n",
     "        if (pos != -1):\n",
     "            seq = seq[:pos] + seq[pos + len(utr):]\n",
-    "    if (t == transcript_id):\n",
-    "        print(t, len(trans_utr[t]),trans_utr[t])\n",
+    "    #print(t, len(trans_utr[t]),trans_utr[t])\n",
     "a = seq"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": 21,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -635,12 +678,12 @@
     "\n",
     "a = '''GCTCAGTCCTCCAGGCGTCGGTACTCAGCGGTGTTGGAACTTCGTTGCTTGCTTGCCTGTGCGCGCGTGCGCGGACATGGCCTCAAACGATTATACCCAACAAGCAACCCAAAGCTATGGGGCCTACCCCACCCAGCCCGGGCAGGGCTATTCCCAGCAGAGCAGTCAGCCCTACGGACAGCAGAGTTACAGTGGTTATAGCCAGTCCACGGACACTTCAGGCTATGGCCAGAGCAGCTATTCTTCTTATGGCCAGAGCCAGAACACAGGCTATGGAACTCAGTCAACTCCCCAGGGATATGGCTCGACTGGCGGCTATGGCAGTAGCCAGAGCTCCCAATCGTCTTACGGGCAGCAGTCCTCCTACCCTGGCTATGGCCAGCAGCCAGCTCCCAGCAGCACCTCGGGAAGTTACGGTAGCAGTTCTCAGAGCAGCAGCTATGGGCAGCCCCAGAGTGGGAGCTACAGCCAGCAGCCTAGCTATGGTGGACAGCAGCAAAGCTATGGACAGCAGCAAAGCTATAATCCCCCTCAGGGCTATGGACAGCAGAACCAGTACAACAGCAGCAGTGGTGGTGGAGGTGGAGGTGGAGGTGGAGGTAACTATGGCCAAGATCAATCCTCCATGAGTAGTGGTGGTGGCAGTGGTGGCGGTTATGGCAATCAAGACCAGAGTGGTGGAGGTGGCAGCGGTGGCTATGGACAGCAGGACCGTGGAGGCCGCGGCAGGGGTGGCAGTGGTGGCGGCGGCGGCGGCGGCGGTGGTGGTTACAACCGCAGCAGTGGTGGCTATGAACCCAGAGGTCGTGGAGGTGGCCGTGGAGGCAGAGGTGGCATGGGGTAGGTGTCTCATGAGCCAGGGAGTATCTTTGGTGGGGAGTGTGGAGGATTGCATGAATCTCCCTGAAGCCAGTCCCTAGTGCATGGTTTAGTATTCTTGTTGTCTAGGGATCTGTGAGGGCTTTGATTTGGGGGCAGTGACTTTCTTTTTACATCCCCATTTTATTTTTGTGAGAACTTGGGAGCCTGAACTCCCATCCATACCACTGAATAGAGATTTTGAGTAATGATACTTGTTTCCAAAAAAAAAGAAACCATACATAGATACGTATGGATTGGAGTCATTAATATCCTAGGCAAGAAACATGGAAGTGAAGACTTCTTTCTCTGCAAGGGAAACCGATGATCCCACTCCTGGGAAATAGTAGGGAAACTTGGTATGTGTATTCCCATGTGTCCTCTAGGGAGTTGGTAATGGTTAACCTGACTTCAGCTTCCAGGAATTGGCTACTCTTCCCGTTTTCTATAGTCATTTGAATCCACGAGCTTGATTTGCACTAATTTGACCGACATTGATTTTGTGTGTGACTTGGTTTATGGGGCCAGCTGACTGAAGTAAGCAGACCTTTTGGGCAAAAATATGCTTTGACAGTGGTCTCCCACCTATTTGTTCCACTGTCTGCCTTCCCCTGGTTACTTAAAATTCATCAGCTTGTCCAACTGGACCTTCTTTCCTTCCTGCTGAAGTTGATTTGAAGTAAAACCTTAGATTTGATGTTAAAACAGTTGTCAAATCTGTTGGTAAATAAGATTTGAAGGACCCTACTCTGTCTCCCTTGAAAAAGGGGAGGAATGTCAGTGTTACTGTTTTTGGAAAAAGTAGATTTTTAAACCGAGTTTGGAAATGGTAAGTATGCAGAGGTGGGTGGGGGCAATCTCAAAAACGTGCAAAAATGAGGAAAACAAAAATGAGGAAATGTGTGCGTGTGTTTAATGCAAAACTTTAAAAAGAAAAACAACTGTTATGTGACTGTTAACTTGCTCTGCATTTTATGTGCCACAGGTATGAAAGGTGACATTGCAAAATACTCCGCTCTTCTCGCAGTGTAGAAGGGGTGACCCCGGGGGTTGGGGGAGATCAAAAACAGCTCAGTAGTTAGGACAGAGCTTAGCTAAGTTTGTCTTGCTTTAAGGGGAAGTTGCCTTTGGTTTTGACTTTTTATGGAATGGGGTTGGGTCTGCTTGCTGCTTTCAAAGCAAAAACCACAAAAATGTGTTCAAGGCTACCCCAGCCTGGTGTGAAATGTCTTCTGGGTAAATTGGGGTAGGGTTTTTAAACCAACTACTTGGTTGTCAACCACTTGCGACAAGAGGAAAAAAAAACATCTGCTCCATCGGAAGAACGACCAAGGAAAATGGGTTATTTTTTTTCCAGAGGAAATAGATAACGTAACCTTTTAAAGCAAAATCTTTATAAACTGTGTCTGAGAAATTGCACACGTGTGTGTGACATGCTCAAAGGTCAGACAAGGGGTGGTCAGGAAGGGATGTATTTTAGTAGCCACTTGTATCTTTTTCCAAAAACACCTACCCATGTTTGGGGAATGTTAAACAAAATCAAAAAACAACCTTTTGTAGCCGTTGGAAGCTTCATGTCCTTTCTTCTAACTTGTCTTCTCCAGCGGAAGTGACCGTGGTGGCTTCAATAAATTTGGTGGTAAGTGAACAGAGTTTCCAAAATTCCCAACTCCCAGCAATGCTTTGTCTGATTGTTCATTTGCAGATGTCTTAGCGTGTTAATTTAAATGTCAAAGGTTTTGAGGTGTCCAGAACCACCTCCAGAAAGGGGTAGGGTAGAATGCCACCTGTTGCCTGGTGTGTGCTAACCTGGAGCAGGTAGGGGTAAGACTCAATAGTCATCTTTTACCAAATGGGTTTGCCCCAGGTTAATAAGAGGGGTCTAGTAGGCCTTGGACTGGGCCGTTGCCACACCTGGCACTTAGTGACCATCATCATGAGAAACTGGAGAGTGCGTGCTGGAACACGTGGTGCCATCTTGGCTTTAGGATCCTTTTGATCGTTGTGTCCAAGGCTTGTGTGTGTGTGAGTGTGTGGGAGACAACTCCGAATGTTTAATTCTGGAAGAGGGATGTAACATTGCCCTGAGGATGGTGAAGTTGGTATACATTTATAAAGTACGGAATGGTGTCAATGAATGCAATTCTATGTATATGGACTTAACTGAGATGGGCAAATAGAAACTAGCTCTGGGAAGGAACATGTGCACTACTTCAAGAAAGATTGGAAGCATGTGTGGCTCATGGGAAATAACCAGGTCTTAAACAGCACAAACTGAATTCGTGGACCAGGAAGGTCTTAAACAGCACAAACTGAATTCATGGAAAAATGACAAATTTGAGAAGTCTCCCAGTAAGCTGGAACTTTTCTGGTTTGGTTAACAAAAGGTTTCTTGATTTGTTTCAAGATTTAAAGCCAAAGGTGTGGGTTCATGACTTAGGTGTCATTGCGTGTGGGTACAATATTTATATATGGCGAATTCAGATAAACATTGGTCAAAGATGGTCTCTGGAAAAACAAAATAGAGGCTGCATTACGGAAATAAGATTTCTGGTCTGTTCCCTGGGACATGCTTAAAAAATACAATAGCTATTATGTATGGTTTTTATTTTCATGTGGTTTCGGGGAAACAACACGGTTTTAAGGATGGTTTCTAAAGATGAAATTAAAAATTGTTCCACAAGGGTTAAGTGTCTGGTGGTAAAGTTGGGAGAAACTGGATGGATGCACATCGCATGGCTGGTGGCGAGCCCATCTCTCTTCTCTCGGGTGAGAGAACCGGGCCAAGCTGAGTTGGTTTGTTCACTTTAATGGGTCTCCGTTTCCCCTGCCACCTGTGCTGAGGACATTTCCCAGCCTGAGCTGGGGGAGGCAGCATTTGCTGAAGTGTGGAGTTGTCTCTGTGGAGACTCAAGTTACAGATCTTAAGGGGCCTGCCTAGAATTTTCTCCTCTGGGCAGGCGACCCAGGAAAGGGTTTGGAGTGAGGCTGTGAGCACTTACTTGATATTTTACAAGTTTGGATTTGGTGTTAATTTTTTTCCTTGTCCGTTTTTTCCTGTTGACTAACGGCTCATCTTTTCCTTGTTTTTGTTTTTTTTTTGTTCTTTTTTTCCATGTCACTAAAGGCCCTCGGGACCAAGGATCACGTCATGACTCCGAACAGGATAATTCAGACAACAACACCATCTTTGTGCAAGGCCTGGGTGAGAATGTTACAATTGAGTCTGTGGCTGATTACTTCAAGCAGATTGGTATTATTAAGACAAACAAGAAAACGGGACAGCCCATGATTAATTTGTACACAGACAGGGAAACTGGCAAGCTGAAGGGAGAGGCAACGGTCTCTTTTGATGACCCACCTTCAGCTAAAGCAGCTATTGACTGGTTTGATGGTAAAGAATTCTCCGGAAATCCTATCAAGGTCTCATTTGCTACTCGCCGGGCAGACTTTAATCGGGGTGGTGGCAATGGTCGTGGAGGCCGAGGGCGAGGAGGACCCATGGGCCGTGGAGGCTATGGAGGTGGTGGCAGTGGTGGTGGTGGCCGAGGAGGATTTCCCAGTGGAGGTGGTGGCGGTGGAGGACAGCAGCGAGCTGGTGACTGGAAGTGTCCTAATCCCACCTGTGAGAATATGAACTTCTCTTGGAGGAATGAATGCAACCAGTGTAAGGCCCCTAAACCAGATGGCCCAGGAGGGGGACCAGGTGGCTCTCACATGGGGGGTAACTACGGGGATGATCGTCGTGGTGGCAGAGGAGGCTATGATCGAGGCGGCTACCGGGGCCGCGGCGGGGACCGTGGAGGCTTCCGAGGGGGCCGGGGTGGTGGGGACAGAGGTGGCTTTGGCCCTGGCAAGATGGATTCCAGGGGTGAGCACAGACAGGATCGCAGGGAGAGGCCGTATTAATTAGCCTGGCTCCCCAGGTTCTGGAACAGCTTTTTGTCCTGTACCCAGTGTTACCCTCGTTATTTTGTAACCTTCCAATTCCTGATCACCCAAGGGTTTTTTTGTGTCGGACTATGTAATTGTAACTATACCTCTGGTTCCCATTAAAAGTGACCATTTTAGTTAAA'''\n",
     "\n",
-    "a = '''GGTGACAACGGCAACATGGCCCTGAACGGAGCTGGTGAGGACCTGGGCGGCAGGGGTTTGTGGCTGTGAGGTACGGGAGGCAGCCCACTCCGGCAAGACCCCCAGTCCCTATGCCTCTCTTCCCCAGAAGTCGACGACTTCTCCTGGGAGCCCCCGACTGAGGCGGAGACGAAGACGATCCTCCTCCAAGACAAACAGCGGAAAATCTACTGCGTGGCTTGTCAGGAACTCGACTCAGACGTGGATAAAGATAATCCCGCTCTGAATGCCCAGGCTGCCCTCTCCCAAGCTCGGGAGCACCAGCTGGCCTCAGCCTCAGAGCTCCCCCTGGGCTCTCGACCTGCGCCCCAGCCCCCAGTACCTCGTCCGGAGCACTGTGAGGGAGCTGCAGCAGGACTCAAGGCAGCCCAGGGGCCACCTGCTCCTGCTGTGCCTCCAAATACAGATGTCATGGCCTGCACACAGACAGCCCTCTTGCAGAAGCTGACCTGGGCCTCTGCTGAACTGGGCTCTAGCACCTCCCTGGAGACTAGCATCCAGCTGTGTGGCCTTATCCGCGCATGTGCGGAGGCCCTGCGCAGCCTGCAGCAGCTACAGCACTAAGAGAAGCCCCTGAGAAAAACCCTCTAGAAAAA'''"
+    "a = '''AGTGCGGAGCCTTAGGCGGAGCGAAGAGAACCGGTCGCGGCAATCCTAGCGCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCCGCATCCGCTGCGGGAGTCCGAGCCGGAACCACACCCAAGTAGCTGCCCTTTCCTCTTCTGTCATCTCACCGCCCCACCACAGACCGCGTTCCCCGAGGAAACCGGCCGCCCACGCCCGGAGCATCCTCCCCTGTTGAGCGGGCGCTGACGGACCCGGCGGCATGATGCGGCTGCGAGGCTCGGGGATGCTGCGGGACCTGCTCCTGCGGTCGCCCGCCGGCGTGAGCGCGACTCTGCGGCGGGCACAGCCCTTGGTCACCCTGTGCCGGCGTCCCCGAGGCGGGGGACGGCCGGCCGCGGGCCCGGCTGCCGCCGCGCGACTCCACCCGTGGTGGGGCGGGGGCGGCTGGCCGGCGGAGCCCCTCGCGCGGGGCCTGTCCAGCTCTCCTTCGGAGATCTTGCAGGAGCTGGGCAAGGGGAGCACGCATCCGCAGCCCGGGGTGTCGCCACCCGCTGCCCCGGCGGCGCCCGGCCCCAAGGACGGCCCCGGGGAGACGGACGCGTTTGGCAACAGCGAGGGCAAAGAGCTGGTGGCCTCAGGTGAAAATAAAATAAAACAGGGTCTGTTACCTAGCTTGGAAGATTTGCTGTTCTATACAATTGCTGAAGGACAAGAGAAAATACCTGTTCATAAATTTATTACAGCACTCAAATCTACAGGATTGCGAACGTCTGATCCCAGGTTGAAAGAGTGTATGGATATGTTAAGATTAACTCTTCAAACAACATCAGATGGTGTCATGCTAGACAAAGATCTTTTTAAAAAATGTGTTCAGAGCAACATTGTTTTGTTGACACAAGCATTTAGAAGAAAGTTTGTGATTCCTGACTTTATGTCTTTTACCTCACACATTGATGAGTTATATGAAAGTGCTAAAAAGCAGTCTGGAGGAAAGGTTGCAGATTATATTCCTCAACTGGCCAAATTCAGTCCCGATTTGTGGGGTGTGTCTGTTTGTACAGTAGATGGACAGAGGCATTCTACTGGAGATACCAAAGTTCCCTTCTGTCTTCAGTCCTGTGTAAAACCTTTGAAATATGCCATTGCTGTTAATGATCTTGGAACTGAATATGTGCATCGATATGTTGGAAAAGAGCCGAGTGGACTAAGATTCAACAAACTATTTTTGAATGAAGATGATAAACCACATAATCCTATGGTAAATGCTGGAGCAATTGTTGTGACTTCACTAATAAAGCAAGGAGTAAATAATGCTGAAAAATTTGACTATGTCATGCAGTTTTTGAATAAGATGGCTGGTAATGAATATGTTGGATTCAGTAATGCAACGTTTCAGTCTGAAAGAGAAAGTGGAGATCGAAATTTTGCAATAGGATATTACTTAAAAGAAAAGAAGTGTTTTCCAGAAGGCACAGACATGGTTGGTATATTAGACTTCTACTTCCAGCTGTGCTCCATTGAAGTGACTTGTGAATCAGCCAGTGTGATGGCTGCGACACTGGCTAATGGTGGTTTCTGCCCAATTACTGGTGAAAGAGTACTGAGCCCTGAAGCAGTTCGAAATACATTGAGTTTGATGCATTCCTGTGGCATGTATGACTTCTCAGGGCAGTTTGCTTTCCATGTTGGTCTTCCTGCAAAATCTGGAGTTGCTGGGGGCATTCTTTTAGTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTAAGGGAATTCACTTTTGTCACGATCTTGTTTCTCTGTGTAATTTCCATAACTATGATAATTTGAGACACTTTGCAAAAAAACTTGATCCTCGAAGAGAAGGTGGTGATCAAAGGGTAAAGTCAGTGATAAATCTTTTGTTTGCTGCATATACTGGAGATGTGTCTGCACTTCGAAGATTTGCTTTGTCAGCTATGGACATGGAACAGCGGGACTATGATTCTAGAACAGCACTCCATGTAGCTGCTGCAGAGGGTCATGTTGAAGTTGTTAAATTTTTGCTGGAAGCCTGCAAAGTAAACCCTTTCCCCAAGGACAGGTGGAATAACACTCCCATGGATGAAGCACTGCACTTTGGACACCATGATGTATTTAAAATTCTCCAAGAATACCAAGTCCAGTACACACCTCAAGGAGATTCTGACAACGGGAAGGAAAATCAAACCGTCCATAAGAATCTTGATGGATTGTTGTAATGGTCTCAAATCCCAAGATTTAAATCACTTACCTATTTAATTGTGGAAAATGATTATGAAGAACATGTGTATTTCTATCTGGTAGTGATGTATATTTTACATTTGTCATTTCAGTGTTACTGGAGTTTTCTTCATTGTGCACACAGGACAAATCTGATCTCTTTGGGAAAAAATAGAAATAAAACAATCTCCCTCCATAATGTGAGCAATATTACCTCGTGCATTGTATAATTTGATGTAAAAGAAATAGTTACCAATGCTAGCTTGTGTGGTCTTCCATGATTTATTTGTGTTTTGTGAATTTTCAATTTATGGTGATGATCTGCTGATATGCATTTATAAAGTAAGCTCTGTTGTACAGTCTGTCCAAATGGGTCAAGGTTGCCTTTAGAAGCAAATAGTGTGATTTTCAAGACTTCAAATACAAATTTAGTTTAAGTGTTTGAACAACTATATGCACTTACGGTTGTGTGTTTAAAATGTCTCTCTCACCCCCTAGCTTCATGATGTGACTCTTAAAAAACTATAATAGTTAACAACTGTTAGTAAGATAGACCAATTCTGATTAGACTTTATCAGGGAATCTGTTTAAGATATGTTTGGTGACCAAAACGTATGTGTGAATGTAGTTATAATGCTTTTGAAAAATTTTCCTTTTTCTATATCCCCTTAGTCCAGCCTCTCTTCTCAGACATTTAGCTATCTGCCTCTTTCCTTTAGCTGGGAAAGTGAGAGCTGGCATACTATGCAGTTTTTATGTTTTCCATAGTAAGTCAGAAAATGCCTCCTATTTCTGGCATCAGAACTTTGCCATTTGTCTACAGAAGACGAACCAGAGACAAAATTACTAAGTATAAATTAGTCAAGTTTATCAGTCTAAAAAACGAAGGGATGTGCAACTGCAGCTCTTTAAGAAGTTTTTTTTTTTTAGCTTCTAGGGTAAAGATAAATTCAGAAATGCTCTAAGCTACCAAAGTTATTCTGAAAGTATGGGAACTGCTACAACTAACAAACATTTGTTTCCAAGCCTGTCATTAAGAGTCTGCATCAAGAGATTTGTCCTCCTTGGGGGACCACTGGATCATTCCAGATTTCTTGTGATTTTTCTATTGTGTAATTCTTGGTGGGCTCTGTAGTTTAATAATAAGAAAAAGGCCATTTCATTTTAAATTGTGACCTATAATTCTTTGTCTTGGGTTGGTAATTCAGGATTCATTTGGAAAGTGGGTAAAAGGGGCTTCAAAAAACGGATAGAACAGGATTTTCTAGGAGTTACACATACATTTTATCCTGTCATACCTCGAGATAAAGTGGCATGTTAGTGAGGAGTTCTGATATTAAGCACACACACACATGCACACAAATGGACTTCTCTGAAGCTGTGTTTAGTGAAATGAGCTCAAGTACATGAATGTTAGTTGTTATCACATACAGCAAATTCCTTTTTTTTTCTTTTTCTATGAGCACACTCTGCTGCTTCTAAACTTTACATGCCTGATGGCACCTTACTCCAGCAGCCTCCAGGTGCTTTCATTTTCACTTCCAGTCTAAGCCAGTGGCTCCTGCCACTGCCCTCCCATTACCTAGATGGCACCTCCTTTGGTGAAACCACGGCCAATGTTCCTTAGCTGCACCAGGCCCGAAGCTGTTCCCATGCTTGAGCTTCCATGGGGAGGATGCTGAGTGAGCAGTTTCCTACCCCGTGGATCTAGCAAGCCATGGAGACAGGTAGCATTTGTAAGATGCTGCACAGGAGCAGCATTATCCCCAAAGATATTACAGGGTAGACACGTTTTAACTGAAATCAATCAAGATAACTTTATTCAAAGAGCAGCCCGCTTTGTGTGACTAAAATGAAACAAGACAGTTGAATTGTGTGACTTGAAGATTACCAATGATTTTGAGGCTTTTCTATAATAAAAAGAGGTTCTAACCATTATTTGGGAACAAAGAGAGTTTTCATCTTTTTTCAGATCAAAACCATTCTGTAAAATCTTTGTTGTTTAATTAAATGTGCCGTTATTTACCCCTGATGTTATTTATGACTATGTGCCGATTCCTGCTCGGGCTGTTTGCTGTTGGCTGGTAATAATATATTTGATTTAAATGCTGTTGACTGTGCTATTAACTGCTGCCGTCAGTAAACTCCAAAGATCTTTTTGTTTTGGCTTTAGTATCATATGTGCTTTTTCTGTATCCTGAGCGCTCTATATGATCATGTTAATTTAAAGCTTTATACACATTGTTGTTTTTGCTGGTCTCATCTTTGGTAATATGCTATACCCCACTGCTGCCCGACACTGCCCTTTAGCTGCAGAGCTGGATTAGCTGTTGACCATTTGATGCTGTTGTCTGTCTGGCAGGGACTGAATGACCTGATGTCAGATTTAGATTCTTCCTGGGGATTACACAGCTATGAATGTATTTGCTTCTAAAACCTCCCAAAGTGAATCTAATCTTAAAACTACAAGTTGTAAGTATTCTGAAATTGGGAAACATTTATTTTAAATGCAATCAGGTAGTGTTGCTTTTTACAGCATAATAAATATATGTATCAAAAAAAAAA'''"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": 22,
    "metadata": {
     "scrolled": true
    },
@@ -649,9 +692,9 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "GDNGNM+ALNGAGEDLGGRGLWL_GTGGSPLRQDPQSLCLSSPEVDDFSWEPPTEAETKTILLQDKQRKIYCVACQELDSDVDKDNPALNAQAALSQAREHQLASASELPLGSRPAPQPPVPRPEHCEGAAAGLKAAQGPPAPAVPPNTDVM+ACTQTALLQKLTWASAELGSSTSLETSIQLCGLIRACAEALRSLQQLQH_EKPLRKTL_K\n",
-      "VTTATWP_TELVRTWAAGVCGCEVREAAHSGKTPSPYASLPQKSTTSPGSPRLRRRRRRSSSKTNSGKSTAWLVRNSTQTWIKIIPL_M+PRLPSPKLGSTSWPQPQSSPWALDLRPSPQYLVRSTVRELQQDSRQPRGHLLLLCLQIQM+SWPAHRQPSCRS_PGPLLNWALAPPWRLASSCVALSAHVRRPCAACSSYSTKRSP_EKPSRK\n",
-      "_QRQHGPERSW_GPGRQGFVAVRYGRQPTPARPPVPM+PLFPRSRRLLLGAPD_GGDEDDPPPRQTAENLLRGLSGTRLRRG_R_SRSECPGCPLPSSGAPAGLSLRAPPGLSTCAPAPSTSSGAL_GSCSRTQGSPGATCSCCASKYRCHGLHTDSPLAEADLGLC_TGL_HLPGD_HPAVWPYPRM+CGGPAQPAAATALREAPEKNPLEK\n"
+      "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"
      ]
     }
    ],
@@ -700,26 +743,226 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 184,
+   "execution_count": 118,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL\n",
+      "MVSC\n",
+      "MCSEQHCFVDTSI\n"
+     ]
+    }
+   ],
+   "source": [
+    "def translate(seq,orf):\n",
+    "    seq = seq.upper()\n",
+    "    seq = seq.replace(\"\\n\",\"\")\n",
+    "\n",
+    "    table = { \n",
+    "        'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', \n",
+    "        'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', \n",
+    "        'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', \n",
+    "        'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',                  \n",
+    "        'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', \n",
+    "        'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', \n",
+    "        'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', \n",
+    "        'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', \n",
+    "        'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', \n",
+    "        'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', \n",
+    "        'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', \n",
+    "        'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', \n",
+    "        'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', \n",
+    "        'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L', \n",
+    "        'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_', \n",
+    "        'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W', \n",
+    "    } \n",
+    "\n",
+    "    protein = \"\"\n",
+    "    exon = False\n",
+    "    translating = True\n",
+    "    i = orf\n",
+    "\n",
+    "    while (translating):\n",
+    "        codon = seq[i:i+3]\n",
+    "        \n",
+    "        try: table[codon]\n",
+    "        except: break\n",
+    "\n",
+    "        if (table[codon] == \"M\"):\n",
+    "            exon = True\n",
+    "\n",
+    "        if (exon):\n",
+    "            if (table[codon] == \"_\"):\n",
+    "                exon = False\n",
+    "                translating = False\n",
+    "            else:\n",
+    "                protein += table[codon]\n",
+    "                i += 3\n",
+    "        else:\n",
+    "            i += 3\n",
+    "            \n",
+    "    return protein\n",
+    "\n",
+    "a = \"AGTGCGGAGCCTTAGGCGGAGCGAAGAGAACCGGTCGCGGCAATCCTAGCGCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCCGCATCCGCTGCGGGAGTCCGAGCCGGAACCACACCCAAGTAGCTGCCCTTTCCTCTTCTGTCATCTCACCGCCCCACCACAGACCGCGTTCCCCGAGGAAACCGGCCGCCCACGCCCGGAGCATCCTCCCCTGTTGAGCGGGCGCTGACGGACCCGGCGGCATGATGCGGCTGCGAGGCTCGGGGATGCTGCGGGACCTGCTCCTGCGGTCGCCCGCCGGCGTGAGCGCGACTCTGCGGCGGGCACAGCCCTTGGTCACCCTGTGCCGGCGTCCCCGAGGCGGGGGACGGCCGGCCGCGGGCCCGGCTGCCGCCGCGCGACTCCACCCGTGGTGGGGCGGGGGCGGCTGGCCGGCGGAGCCCCTCGCGCGGGGCCTGTCCAGCTCTCCTTCGGAGATCTTGCAGGAGCTGGGCAAGGGGAGCACGCATCCGCAGCCCGGGGTGTCGCCACCCGCTGCCCCGGCGGCGCCCGGCCCCAAGGACGGCCCCGGGGAGACGGACGCGTTTGGCAACAGCGAGGGCAAAGAGCTGGTGGCCTCAGGTGAAAATAAAATAAAACAGGGTCTGTTACCTAGCTTGGAAGATTTGCTGTTCTATACAATTGCTGAAGGACAAGAGAAAATACCTGTTCATAAATTTATTACAGCACTCAAATCTACAGGATTGCGAACGTCTGATCCCAGGTTGAAAGAGTGTATGGATATGTTAAGATTAACTCTTCAAACAACATCAGATGGTGTCATGCTAGACAAAGATCTTTTTAAAAAATGTGTTCAGAGCAACATTGTTTTGTTGACACAAGCATTTAGAAGAAAGTTTGTGATTCCTGACTTTATGTCTTTTACCTCACACATTGATGAGTTATATGAAAGTGCTAAAAAGCAGTCTGGAGGAAAGGTTGCAGATTATATTCCTCAACTGGCCAAATTCAGTCCCGATTTGTGGGGTGTGTCTGTTTGTACAGTAGATGGACAGAGGCATTCTACTGGAGATACCAAAGTTCCCTTCTGTCTTCAGTCCTGTGTAAAACCTTTGAAATATGCCATTGCTGTTAATGATCTTGGAACTGAATATGTGCATCGATATGTTGGAAAAGAGCCGAGTGGACTAAGATTCAACAAACTATTTTTGAATGAAGATGATAAACCACATAATCCTATGGTAAATGCTGGAGCAATTGTTGTGACTTCACTAATAAAGCAAGGAGTAAATAATGCTGAAAAATTTGACTATGTCATGCAGTTTTTGAATAAGATGGCTGGTAATGAATATGTTGGATTCAGTAATGCAACGTTTCAGTCTGAAAGAGAAAGTGGAGATCGAAATTTTGCAATAGGATATTACTTAAAAGAAAAGAAGTGTTTTCCAGAAGGCACAGACATGGTTGGTATATTAGACTTCTACTTCCAGCTGTGCTCCATTGAAGTGACTTGTGAATCAGCCAGTGTGATGGCTGCGACACTGGCTAATGGTGGTTTCTGCCCAATTACTGGTGAAAGAGTACTGAGCCCTGAAGCAGTTCGAAATACATTGAGTTTGATGCATTCCTGTGGCATGTATGACTTCTCAGGGCAGTTTGCTTTCCATGTTGGTCTTCCTGCAAAATCTGGAGTTGCTGGGGGCATTCTTTTAGTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTAAGGGAATTCACTTTTGTCACGATCTTGTTTCTCTGTGTAATTTCCATAACTATGATAATTTGAGACACTTTGCAAAAAAACTTGATCCTCGAAGAGAAGGTGGTGATCAAAGGGTAAAGTCAGTGATAAATCTTTTGTTTGCTGCATATACTGGAGATGTGTCTGCACTTCGAAGATTTGCTTTGTCAGCTATGGACATGGAACAGCGGGACTATGATTCTAGAACAGCACTCCATGTAGCTGCTGCAGAGGGTCATGTTGAAGTTGTTAAATTTTTGCTGGAAGCCTGCAAAGTAAACCCTTTCCCCAAGGACAGGTGGAATAACACTCCCATGGATGAAGCACTGCACTTTGGACACCATGATGTATTTAAAATTCTCCAAGAATACCAAGTCCAGTACACACCTCAAGGAGATTCTGACAACGGGAAGGAAAATCAAACCGTCCATAAGAATCTTGATGGATTGTTGT\"\n",
+    "print(translate(a,0))\n",
+    "print(translate(a,1))\n",
+    "print(translate(a,2))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 160,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "264 CGGCATGA MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL 0.003137706\n"
+     ]
+    },
     {
      "data": {
       "text/plain": [
-       "4437"
+       "'MMRLRGSGMLRDLLLRSPAGVSATLRRAQPLVTLCRRPRGGGRPAAGPAAAARLHPWWGGGGWPAEPLARGLSSSPSEILQELGKGSTHPQPGVSPPAAPAAPGPKDGPGETDAFGNSEGKELVASGENKIKQGLLPSLEDLLFYTIAEGQEKIPVHKFITALKSTGLRTSDPRLKECMDMLRLTLQTTSDGVMLDKDLFKKCVQSNIVLLTQAFRRKFVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYDNLRHFAKKLDPRREGGDQRVKSVINLLFAAYTGDVSALRRFALSAMDMEQRDYDSRTALHVAAAEGHVEVVKFLLEACKVNPFPKDRWNNTPMDEALHFGHHDVFKILQEYQVQYTPQGDSDNGKENQTVHKNLDGLL'"
       ]
      },
-     "execution_count": 184,
+     "execution_count": 160,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "a.find(\"\n",
-    "       \n",
-    "       \")"
+    "codon_table = {\n",
+    "        'ATA':'I', 'ATC':'I', 'ATT':'I', 'ATG':'M', \n",
+    "        'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T', \n",
+    "        'AAC':'N', 'AAT':'N', 'AAA':'K', 'AAG':'K', \n",
+    "        'AGC':'S', 'AGT':'S', 'AGA':'R', 'AGG':'R',                  \n",
+    "        'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', \n",
+    "        'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', \n",
+    "        'CAC':'H', 'CAT':'H', 'CAA':'Q', 'CAG':'Q', \n",
+    "        'CGA':'R', 'CGC':'R', 'CGG':'R', 'CGT':'R', \n",
+    "        'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', \n",
+    "        'GCA':'A', 'GCC':'A', 'GCG':'A', 'GCT':'A', \n",
+    "        'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E', \n",
+    "        'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', \n",
+    "        'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', \n",
+    "        'TTC':'F', 'TTT':'F', 'TTA':'L', 'TTG':'L', \n",
+    "        'TAC':'Y', 'TAT':'Y', 'TAA':'_', 'TAG':'_', \n",
+    "        'TGC':'C', 'TGT':'C', 'TGA':'_', 'TGG':'W', \n",
+    "        }\n",
+    "\n",
+    "def determine_utrs(gene):\n",
+    "    filename = \"/home/annaldas/projects/result/%s/%s_utr_regions.fa\" %(gene,gene)\n",
+    "    bedfastafile = open(filename,\"r\")\n",
+    "    bedfastalines = bedfastafile.readlines()\n",
+    "    bedfastafile.close()\n",
+    "    gene_utr = dict()\n",
+    "    for line in bedfastalines:\n",
+    "        if (line.startswith(\">\")):\n",
+    "            trans_id = line[1:].strip()\n",
+    "            if (trans_id not in gene_utr):\n",
+    "                gene_utr[trans_id] = []\n",
+    "        else:\n",
+    "            gene_utr[trans_id].append(line.strip())\n",
+    "    return gene_utr\n",
+    "\n",
+    "def score(seq,start):    \n",
+    "    kozak = {\n",
+    "        \"A\":[0.25,0.61,0.27,0.15,1.00,0.00,0.00,0.23],\n",
+    "        \"C\":[0.53,0.02,0.49,0.55,0.00,0.00,0.00,0.16],\n",
+    "        \"G\":[0.15,0.36,0.13,0.21,0.00,0.00,1.00,0.46],\n",
+    "        \"T\":[0.07,0.01,0.11,0.09,0.00,1.00,0.00,0.15]\n",
+    "    }\n",
+    "    \n",
+    "    score = 1.0\n",
+    "    for i in range(start,len(seq)):\n",
+    "        score *= kozak[seq[i]][i]\n",
+    "    return score\n",
+    "        \n",
+    "\n",
+    "def translate(seq, i, utr_regions):\n",
+    "    translating = True\n",
+    "    aa = \"\"\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",
+    "        else:\n",
+    "            codon = seq[0:3]\n",
+    "            if (codon_table[codon] == \"_\"):\n",
+    "                translating = False\n",
+    "            else:\n",
+    "                aa += codon_table[codon]\n",
+    "            seq = seq[3:]\n",
+    "            i += 3\n",
+    "    return aa\n",
+    "\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",
+    "        if (pos != -1):\n",
+    "            utr_regions.append([pos,pos + len(utr)])\n",
+    "    \n",
+    "    longest_aa_seq = \"\"\n",
+    "    longest_aa_seq_sc = 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",
+    "                longest_aa_seq = aa\n",
+    "                longest_aa_seq_sc = sc\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",
+    "    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",
+    "            \n",
+    "    return longest_aa_seq\n",
+    "            \n",
+    "enst = \"ENST00000320717\"\n",
+    "a=\"AGTGCGGAGCCTTAGGCGGAGCGAAGAGAACCGGTCGCGGCAATCCTAGCGCGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCACCCGCATCCGCTGCGGGAGTCCGAGCCGGAACCACACCCAAGTAGCTGCCCTTTCCTCTTCTGTCATCTCACCGCCCCACCACAGACCGCGTTCCCCGAGGAAACCGGCCGCCCACGCCCGGAGCATCCTCCCCTGTTGAGCGGGCGCTGACGGACCCGGCGGCATGATGCGGCTGCGAGGCTCGGGGATGCTGCGGGACCTGCTCCTGCGGTCGCCCGCCGGCGTGAGCGCGACTCTGCGGCGGGCACAGCCCTTGGTCACCCTGTGCCGGCGTCCCCGAGGCGGGGGACGGCCGGCCGCGGGCCCGGCTGCCGCCGCGCGACTCCACCCGTGGTGGGGCGGGGGCGGCTGGCCGGCGGAGCCCCTCGCGCGGGGCCTGTCCAGCTCTCCTTCGGAGATCTTGCAGGAGCTGGGCAAGGGGAGCACGCATCCGCAGCCCGGGGTGTCGCCACCCGCTGCCCCGGCGGCGCCCGGCCCCAAGGACGGCCCCGGGGAGACGGACGCGTTTGGCAACAGCGAGGGCAAAGAGCTGGTGGCCTCAGGTGAAAATAAAATAAAACAGGGTCTGTTACCTAGCTTGGAAGATTTGCTGTTCTATACAATTGCTGAAGGACAAGAGAAAATACCTGTTCATAAATTTATTACAGCACTCAAATCTACAGGATTGCGAACGTCTGATCCCAGGTTGAAAGAGTGTATGGATATGTTAAGATTAACTCTTCAAACAACATCAGATGGTGTCATGCTAGACAAAGATCTTTTTAAAAAATGTGTTCAGAGCAACATTGTTTTGTTGACACAAGCATTTAGAAGAAAGTTTGTGATTCCTGACTTTATGTCTTTTACCTCACACATTGATGAGTTATATGAAAGTGCTAAAAAGCAGTCTGGAGGAAAGGTTGCAGATTATATTCCTCAACTGGCCAAATTCAGTCCCGATTTGTGGGGTGTGTCTGTTTGTACAGTAGATGGACAGAGGCATTCTACTGGAGATACCAAAGTTCCCTTCTGTCTTCAGTCCTGTGTAAAACCTTTGAAATATGCCATTGCTGTTAATGATCTTGGAACTGAATATGTGCATCGATATGTTGGAAAAGAGCCGAGTGGACTAAGATTCAACAAACTATTTTTGAATGAAGATGATAAACCACATAATCCTATGGTAAATGCTGGAGCAATTGTTGTGACTTCACTAATAAAGCAAGGAGTAAATAATGCTGAAAAATTTGACTATGTCATGCAGTTTTTGAATAAGATGGCTGGTAATGAATATGTTGGATTCAGTAATGCAACGTTTCAGTCTGAAAGAGAAAGTGGAGATCGAAATTTTGCAATAGGATATTACTTAAAAGAAAAGAAGTGTTTTCCAGAAGGCACAGACATGGTTGGTATATTAGACTTCTACTTCCAGCTGTGCTCCATTGAAGTGACTTGTGAATCAGCCAGTGTGATGGCTGCGACACTGGCTAATGGTGGTTTCTGCCCAATTACTGGTGAAAGAGTACTGAGCCCTGAAGCAGTTCGAAATACATTGAGTTTGATGCATTCCTGTGGCATGTATGACTTCTCAGGGCAGTTTGCTTTCCATGTTGGTCTTCCTGCAAAATCTGGAGTTGCTGGGGGCATTCTTTTAGTTGTCCCCAATGTTATGGGTATGATGTGCTGGTCTCCTCCTCTGGATAAGATGGGCAACAGTGTTAAGGGAATTCACTTTTGTCACGATCTTGTTTCTCTGTGTAATTTCCATAACTATGATAATTTGAGACACTTTGCAAAAAAACTTGATCCTCGAAGAGAAGGTGGTGATCAAAGGGTAAAGTCAGTGATAAATCTTTTGTTTGCTGCATATACTGGAGATGTGTCTGCACTTCGAAGATTTGCTTTGTCAGCTATGGACATGGAACAGCGGGACTATGATTCTAGAACAGCACTCCATGTAGCTGCTGCAGAGGGTCATGTTGAAGTTGTTAAATTTTTGCTGGAAGCCTGCAAAGTAAACCCTTTCCCCAAGGACAGGTGGAATAACACTCCCATGGATGAAGCACTGCACTTTGGACACCATGATGTATTTAAAATTCTCCAAGAATACCAAGTCCAGTACACACCTCAAGGAGATTCTGACAACGGGAAGGAAAATCAAACCGTCCATAAGAATCTTGATGGATTGTTGTAATGGTCTCAAATCCCAAGATTTAAATCACTTACCTATTTAATTGTGGAAAATGATTATGAAGAACATGTGTATTTCTATCTGGTAGTGATGTATATTTTACATTTGTCATTTCAGTGTTACTGGAGTTTTCTTCATTGTGCACACAGGACAAATCTGATCTCTTTGGGAAAAAATAGAAATAAAACAATCTCCCTCCATAATGTGAGCAATATTACCTCGTGCATTGTATAATTTGATGTAAAAGAAATAGTTACCAATGCTAGCTTGTGTGGTCTTCCATGATTTATTTGTGTTTTGTGAATTTTCAATTTATGGTGATGATCTGCTGATATGCATTTATAAAGTAAGCTCTGTTGTACAGTCTGTCCAAATGGGTCAAGGTTGCCTTTAGAAGCAAATAGTGTGATTTTCAAGACTTCAAATACAAATTTAGTTTAAGTGTTTGAACAACTATATGCACTTACGGTTGTGTGTTTAAAATGTCTCTCTCACCCCCTAGCTTCATGATGTGACTCTTAAAAAACTATAATAGTTAACAACTGTTAGTAAGATAGACCAATTCTGATTAGACTTTATCAGGGAATCTGTTTAAGATATGTTTGGTGACCAAAACGTATGTGTGAATGTAGTTATAATGCTTTTGAAAAATTTTCCTTTTTCTATATCCCCTTAGTCCAGCCTCTCTTCTCAGACATTTAGCTATCTGCCTCTTTCCTTTAGCTGGGAAAGTGAGAGCTGGCATACTATGCAGTTTTTATGTTTTCCATAGTAAGTCAGAAAATGCCTCCTATTTCTGGCATCAGAACTTTGCCATTTGTCTACAGAAGACGAACCAGAGACAAAATTACTAAGTATAAATTAGTCAAGTTTATCAGTCTAAAAAACGAAGGGATGTGCAACTGCAGCTCTTTAAGAAGTTTTTTTTTTTTAGCTTCTAGGGTAAAGATAAATTCAGAAATGCTCTAAGCTACCAAAGTTATTCTGAAAGTATGGGAACTGCTACAACTAACAAACATTTGTTTCCAAGCCTGTCATTAAGAGTCTGCATCAAGAGATTTGTCCTCCTTGGGGGACCACTGGATCATTCCAGATTTCTTGTGATTTTTCTATTGTGTAATTCTTGGTGGGCTCTGTAGTTTAATAATAAGAAAAAGGCCATTTCATTTTAAATTGTGACCTATAATTCTTTGTCTTGGGTTGGTAATTCAGGATTCATTTGGAAAGTGGGTAAAAGGGGCTTCAAAAAACGGATAGAACAGGATTTTCTAGGAGTTACACATACATTTTATCCTGTCATACCTCGAGATAAAGTGGCATGTTAGTGAGGAGTTCTGATATTAAGCACACACACACATGCACACAAATGGACTTCTCTGAAGCTGTGTTTAGTGAAATGAGCTCAAGTACATGAATGTTAGTTGTTATCACATACAGCAAATTCCTTTTTTTTTCTTTTTCTATGAGCACACTCTGCTGCTTCTAAACTTTACATGCCTGATGGCACCTTACTCCAGCAGCCTCCAGGTGCTTTCATTTTCACTTCCAGTCTAAGCCAGTGGCTCCTGCCACTGCCCTCCCATTACCTAGATGGCACCTCCTTTGGTGAAACCACGGCCAATGTTCCTTAGCTGCACCAGGCCCGAAGCTGTTCCCATGCTTGAGCTTCCATGGGGAGGATGCTGAGTGAGCAGTTTCCTACCCCGTGGATCTAGCAAGCCATGGAGACAGGTAGCATTTGTAAGATGCTGCACAGGAGCAGCATTATCCCCAAAGATATTACAGGGTAGACACGTTTTAACTGAAATCAATCAAGATAACTTTATTCAAAGAGCAGCCCGCTTTGTGTGACTAAAATGAAACAAGACAGTTGAATTGTGTGACTTGAAGATTACCAATGATTTTGAGGCTTTTCTATAATAAAAAGAGGTTCTAACCATTATTTGGGAACAAAGAGAGTTTTCATCTTTTTTCAGATCAAAACCATTCTGTAAAATCTTTGTTGTTTAATTAAATGTGCCGTTATTTACCCCTGATGTTATTTATGACTATGTGCCGATTCCTGCTCGGGCTGTTTGCTGTTGGCTGGTAATAATATATTTGATTTAAATGCTGTTGACTGTGCTATTAACTGCTGCCGTCAGTAAACTCCAAAGATCTTTTTGTTTTGGCTTTAGTATCATATGTGCTTTTTCTGTATCCTGAGCGCTCTATATGATCATGTTAATTTAAAGCTTTATACACATTGTTGTTTTTGCTGGTCTCATCTTTGGTAATATGCTATACCCCACTGCTGCCCGACACTGCCCTTTAGCTGCAGAGCTGGATTAGCTGTTGACCATTTGATGCTGTTGTCTGTCTGGCAGGGACTGAATGACCTGATGTCAGATTTAGATTCTTCCTGGGGATTACACAGCTATGAATGTATTTGCTTCTAAAACCTCCCAAAGTGAATCTAATCTTAAAACTACAAGTTGTAAGTATTCTGAAATTGGGAAACATTTATTTTAAATGCAATCAGGTAGTGTTGCTTTTTACAGCATAATAAATATATGTATCAAAAAAAAAA\"\n",
+    "find_all_aa_seqs(a,enst)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "code",
    "execution_count": 18,
@@ -835,6 +1078,13 @@
     "file.close()\n",
     "print(common_domains)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/plotIsoforms.py b/plotIsoforms.py
index a1b2543..cf5442c 100644
--- a/plotIsoforms.py
+++ b/plotIsoforms.py
@@ -117,7 +117,6 @@ def preprocessArguments(args):
     #conditions=list(set([x.split('_')[0] for x in samples]))
     #conditions = ["0","3","5"]
     conditions = ["day0","day3","day5"]
-    print(conditions)
     conditions.sort()
     number_replicates={}
     numerical=True
@@ -162,7 +161,9 @@ def __init__(self, csv, gtf, geneIDs, geneNames, outDir, minTPM, maxIso, minPct)
 (identifier, targets, annotation, data, samples, conditions, number_replicates, x) = preprocessArguments(args)
     
 with PdfPages(outdir+'test.pdf') as pdf:
-    for gene in targets:
+    for gene_ensembl in targets:
+        gene = gene_ensembl.split("_")[0]
+        print(gene)
         df=data[data[identifier]==gene]
         if not df.shape[0]:
             continue
@@ -180,15 +181,16 @@ def __init__(self, csv, gtf, geneIDs, geneNames, outDir, minTPM, maxIso, minPct)
         # 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
+        print(df_temp)
         df_temp=chooseIsoforms2Plot(df_temp,minimumTPM,minimumPct,maximumIso,annotation)
-        
+        x = [0,3,5]
         if df_temp.shape[0]:
             panels = 2
             if (df_temp.shape[0] > 9):
                 panels += 1
             fig,axes = plt.subplots(panels,2,figsize = (12,9)) 
             fig.subplots_adjust(top = 0.9) 
-            fig.suptitle(gene,fontsize=16) 
+            fig.suptitle(gene_ensembl,fontsize=16) 
             #plot isoform expression 
             axg=plt.subplot(panels,2,1) 
             plotProfiles(x, df_temp, data_gene, axg, colors) 
diff --git a/test/list.txt b/test/list.txt
index 3c82b7d..a6957de 100644
--- a/test/list.txt
+++ b/test/list.txt
@@ -1,8 +1,38 @@
-ADAM11
-SST
-SHOX2
-TNC
-GNG8
-IGF2
-REEP1
-CNTFR
+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
diff --git a/test/test.pdf b/test/test.pdf
deleted file mode 100644
index 5cebb3b..0000000
Binary files a/test/test.pdf and /dev/null differ
diff --git a/test/test1.pdf b/test/test1.pdf
deleted file mode 100644
index fb1572f..0000000
Binary files a/test/test1.pdf and /dev/null differ
diff --git a/test/test2.pdf b/test/test2.pdf
deleted file mode 100644
index d1e4219..0000000
Binary files a/test/test2.pdf and /dev/null differ
diff --git a/test/test_all_oldlist.pdf b/test/test_all_oldlist.pdf
deleted file mode 100644
index b24f440..0000000
Binary files a/test/test_all_oldlist.pdf and /dev/null differ
diff --git a/test/test_deseq2.pdf b/test/test_deseq2.pdf
deleted file mode 100644
index 6b3b2d5..0000000
Binary files a/test/test_deseq2.pdf and /dev/null differ
diff --git a/test/test_deseq2_tpm.pdf b/test/test_deseq2_tpm.pdf
deleted file mode 100644
index 1a30353..0000000
Binary files a/test/test_deseq2_tpm.pdf and /dev/null differ
diff --git a/test/test_tpm.pdf b/test/test_tpm.pdf
deleted file mode 100644
index e0ff774..0000000
Binary files a/test/test_tpm.pdf and /dev/null differ
diff --git a/translation_protein.py b/translation_protein.py
index 79c4fdb..1dabda4 100644
--- a/translation_protein.py
+++ b/translation_protein.py
@@ -1,4 +1,5 @@
 from Bio import SeqIO
+import os
 
 def translate(seq,orf):
     seq = seq.upper()
@@ -55,25 +56,46 @@ def translate(seq,orf):
 transcripts = SeqIO.index(transcripts_filename, "fasta")
 output = []
 
+gene = snakemake.input[0].split("/")[5]
+os.mkdir("/home/annaldas/projects/result/%s/transcripts" %(gene))
+
 for transcript in transcripts:
     protein = translate(str(transcripts[transcript].seq),0)
     if (protein != ""):
-        output.append(">" + str(transcripts[transcript].id) + "_1")
-        output.append(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 != ""):
-        output.append(">" + str(transcripts[transcript].id) + "_2")
-        output.append(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 != ""):
-        output.append(">" + str(transcripts[transcript].id) + "_3")
-        output.append(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()
     
-output_filename = snakemake.output[0]
-output_file = open(output_filename,"w+")
-output_file.write("\n".join(output))
-output_file.close()
+#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