diff --git a/src/.docker_modules/kb/0.26.0/t2g.py b/src/.docker_modules/kb/0.26.0/t2g.py index c27cdfa99d454dd80b3c32619a18b9d57f6d22b2..f9f0b45dc89b385c3ed52dc252f8f09eb3bc8c74 100755 --- a/src/.docker_modules/kb/0.26.0/t2g.py +++ b/src/.docker_modules/kb/0.26.0/t2g.py @@ -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" )