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annaldasula
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isoform_differentiation
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Files
bca7730
test
README.md
Snakefile
gene_transcripts.py
genes.tab
interproscan_analysis.py
iso_diff.py
isoform_r.ipynb
isoform_transcripts.ipynb
plotIsoforms.py
protein_transcript_sequences.sh
sashimi-plot.py
sgseq_transcripts.Rmd
shortReadStats.R
transcript_stats.py
translation_protein.py
utr_regions.py
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isoform_differentiation
/
interproscan_analysis.py
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Siddharth Annaldasula
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Feb 10, 2020
bca7730
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Feb 10, 2020
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59 lines (46 loc) · 1.26 KB
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isoform_differentiation
/
interproscan_analysis.py
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59 lines (46 loc) · 1.26 KB
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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)
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