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Commit 8664e1ea authored by Samuel Mondal's avatar Samuel Mondal
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Error correction

parent f50a7708
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1 merge request!8editing pre_bedtools
...@@ -2,14 +2,8 @@ import pandas as pd ...@@ -2,14 +2,8 @@ import pandas as pd
gtf = pd.read_table("Homo_sapiens.GRCh38.107.gtf.gz",skiprows=5,header=None) gtf = pd.read_table("Homo_sapiens.GRCh38.107.gtf.gz",skiprows=5,header=None)
feat = list(gtf[8])
superlist = []
for x in range(len(feat)):
newlist = feat[x].split(";")
superlist.append(newlist)
exons = gtf[gtf[2]=="exon"] exons = gtf[gtf[2]=="exon"]
feat = list(exons[8]) feat = list(exons[8])
superlist = [] superlist = []
idlist = [] idlist = []
...@@ -20,9 +14,6 @@ for x in range(len(feat)): ...@@ -20,9 +14,6 @@ for x in range(len(feat)):
bed = {"chr":exons[0],"start":exons[3],"end":exons[4],"transcript_id":superlist,"score":exons[5],"strand":exons[6],"gene_id":idlist} bed = {"chr":exons[0],"start":exons[3],"end":exons[4],"transcript_id":superlist,"score":exons[5],"strand":exons[6],"gene_id":idlist}
bed = pd.DataFrame(bed) bed = pd.DataFrame(bed)
bed.to_csv("bed_file.bed",sep="\t",index=False) bed.to_csv("bed_file.bed",sep="\t",index=False)
bed[(bed["gene_id"]=="ENSG00000160072")|(bed["gene_id"]== "ENSG00000142611")|(bed["gene_id"]=="ENSG00000232596")].to_csv("test.bed",sep="\t",index=False,header=None)
bed[(bed["gene_id"]=="ENSG00000160072")|(bed["gene_id"]== "ENSG00000142611")|(bed["gene_id"]=="ENSG00000232596")].to_csv("test.bed",sep="\t",index=False,header=None)
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