Extraction of exons from GTF file

sequence_extractor/pre_bedtools.py

+import pandas as pd
+
+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"]   
+    
+feat = list(exons[8])
+superlist = []
+idlist = []
+for x in range(len(feat)):
+    newlist = feat[x].split(";")
+    superlist.append(str(newlist[2])[16:-1])
+    idlist.append(str(newlist[0])[9:-1])
+
+
+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.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)
\ No newline at end of file