Verified Commit 14de29a9 authored by Laurent Modolo's avatar Laurent Modolo
Browse files

t2g.py: fool proof output format

parent fda70fd4
......@@ -3,6 +3,7 @@ import os
import gffutils
import argparse
def validate_file(f):
if not os.path.exists(f):
# Argparse uses the ArgumentTypeError to give a rejection message like:
......@@ -32,10 +33,15 @@ if __name__ == "__main__":
with open("t2g.txt", "w") as t2g:
for gene in db.all_features():
for transcript in db.children(
gene, featuretype='transcript', order_by='start'):
gene, featuretype='transcript', order_by='start'
):
t2g_line = str(transcript["transcript_id"][0]) + \
"\t" + \
str(gene["gene_id"][0])
t2g_line = t2g_line.split("\t")
t2g.write(
str(transcript["transcript_id"][0]) +
str(t2g_line[0].split(".")[0]) +
"\t" +
str(gene["gene_id"][0]) +
str(t2g_line[1].split(".")[0]) +
"\n"
)
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