readGTF split issue

Hi,

Thanks a lot for developing xpore!

I’m working on some non-model organisms, and testing xpore with our own pipeline. The transcripts were assembled with stringtie, and xpore was installed by conda install, the package info is:

# packages in environment at /home/ubuntu/Tools/miniconda3/envs/xpore:
#
# Name                    Version                   Build  Channel
xpore                     2.0                pyh5e36f6f_0    bioconda

and we found stringtie output gtf file was not compatible with xpore. The trackback was like below:

Traceback (most recent call last):
  File "/home/ubuntu/Tools/miniconda3/envs/xpore/bin/xpore", line 10, in <module>
    sys.exit(main())
  File "/home/ubuntu/Tools/miniconda3/envs/xpore/lib/python3.9/site-packages/xpore/scripts/xpore.py", line 67, in main
    options.func(options)
  File "/home/ubuntu/Tools/miniconda3/envs/xpore/lib/python3.9/site-packages/xpore/scripts/dataprep.py", line 692, in dataprep
    gtf_dict = readGTF(gtf_path_or_url)
  File "/home/ubuntu/Tools/miniconda3/envs/xpore/lib/python3.9/site-packages/xpore/scripts/dataprep.py", line 184, in readGTF
    tx_id=ln[-1].split('; transcript_id "')[1].split('";')[0]

By checking the readGTF function, I found this issue may due to a “non-standard” split of gtf attributes (column 9) in readGTF function: https://github.com/GoekeLab/xpore/blob/8722c06314d1fec90dde85347186612144fab6e6/xpore/scripts/dataprep.py#L184-L185

The stringtie gtf has transcript_id as the first attribute, but gene_id as the second, which is not the same as human hg38 gtf file.

example stringtie.gtf:

Gm01	StringTie	transcript	120160	131940	.	+	.	transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; gene_name "MSTRG.3"; xloc "XLOC_000001"; cmp_ref "Glyma.01G000600.2.Wm82.a4.v1"; class_code "="; cmp_ref_gene "Glyma.01G000600.Wm82.a4.v1"; tss_id "TSS1";
Gm01	StringTie	exon	120160	122559	.	+	.	transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "1";
Gm01	StringTie	exon	131469	131940	.	+	.	transcript_id "TCONS_00000001"; gene_id "XLOC_000001"; exon_number "2";

Hope this helps, thanks! obenno

[obenno]

Hi @yuukiiwa,

Thanks a lot for your prompt response.

If you don’t mind, I could do a PR ^^

Best regards, obenno

[obenno]

Hi @yuukiiwa,

Thank you and please feel free to close this issue.