Error in GTFupdate

[lbwfff]

Hi, I want to use a special gtf file and want to process these files through GTFupdate, but I find that there will be some errors.
The following is the content of my gtf file：

chr1	Cufflinks	exon	11872	12227	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000002.2"
chr1	Cufflinks	exon	12613	12721	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000002.2"
chr1	Cufflinks	exon	13225	14412	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000002.2"
chr1	Cufflinks	exon	11874	12227	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000003.2"
chr1	Cufflinks	exon	12595	12721	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000003.2"
chr1	Cufflinks	exon	13403	13655	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000003.2"
chr1	Cufflinks	exon	13661	14409	.	+	.	gene_id "NONHSAG000001.2";gene_name "NONHSAG000001.2";transcript_id "NONHSAT000003.2"

I modified it with reference to the format of GTF_update.rst, but there are still the following errors;

Traceback (most recent call last):
  File "/home/leelee/miniconda3/envs/p3/bin/GTFupdate", line 10, in <module>
    sys.exit(main())
  File "/home/leelee/miniconda3/envs/p3/lib/python3.7/site-packages/RiboCode/GTF_update.py", line 117, in main
    gset,sourted_gset_keys = GroupGeneSubsets(args.gtfFile)
  File "/home/leelee/miniconda3/envs/p3/lib/python3.7/site-packages/RiboCode/GTF_update.py", line 34, in GroupGeneSubsets
    gid=field_dict["attr"]["gene_id"]
KeyError: 'gene_id'

How can i solve this problem？
Thanks,
LeeLee

[zhengtaoxiao]

Hi, have you solved this problem? It seems that the "gene_id" attribute is missing in some lines of GTF file.