Multi-contig gff parsing: Range issue

[acarafat]

Discussed in #32

^{Originally posted by acarafat August 22, 2023}
I am working with a GFF file that contains multiple contigs, but the ##sequence-region only shows for the contig 1 in the gff header info.

Currently, while using .get_seqid2size() from gff parser, present code relies on ##sequence-region tag, therefore it gets the range for rest of the contigs wrong.

It could be solved by not relying on the ##sequence-region, since many gff file generated by different programs may not contain this comment.

[moshi4]

Hi @acarafat,

Thank you for reporting this issue.

Looking back at the code of the Gff parser, as you said, if there is no ##sequence-region tag, it was not getting the contig range correctly.

There was a bug in the code that assumed the absence of the ##sequence-region tag.
Since it does not work as expected, I will release a fixed version as v0.5.1 soon. Please wait a moment.

[moshi4]

I've released v0.5.1, so give it a try and see if it works for you.

[acarafat]

I've released v0.5.1, so give it a try and see if it works for you.

Thank you so much!

[acarafat]

Hello, I'm just realized that the .gbk parser also has the same issue.

Best,
Arafat

[moshi4]

There is no ##sequence-region tag in the Genbank file.
Without additional explanation, I am not sure what same issue means.