Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Manage chevron in GFF start and stop #241

Merged
merged 3 commits into from
Jun 13, 2024
Merged

Manage chevron in GFF start and stop #241

merged 3 commits into from
Jun 13, 2024

Conversation

JeanMainguy
Copy link
Member

In the GFF files, chevrons ('<' or '>') can be found in the start and stop positions to indicate that a gene starts before the beginning of the contig or extends beyond the end of the contig. This special case was previously handled when parsing GBFF files but not in GFF files.

This PR introduces functionality to handle chevrons in GFF files. When chevrons are detected in the start or stop positions, the gene is considered a pseudogene, similar to the behavior implemented for GBFF files.

Example of GFF with chevrons:

GFF_chevrons/822.gff:1574C00058.1	feature	gene	900	>1298	.	+	.	locus_tag=ACIA0v1_580002
GFF_chevrons/822.gff:1574C00058.1	feature	CDS	900	>1298	.	+	0	ID=5549946;db_xref=MicroScope:5549946;ec_number=2.3.1.-;inference=ab initio prediction:AMIGene;locus_tag=ACIA0v1_580002;product=beta-ketoadipyl CoA thiolase %28fragment%29;transl_table=11;translation=MKNAYIIDAIRTPFGRYASGLAPVRADDLGAVPIKALMQRNPSVDWEQVDDVIYGCANQAGEDNRNVGRMSALLAGLPYQVPATTINRLCGSSLDAIAIAARAIKAGEANLVIAGGVESMSRAPYVMGKSDSA

@JeanMainguy
Copy link
Member Author

I added a fake plasmid to the testingDataset repository to test chevron handling using a projection in the CI.

@jpjarnoux jpjarnoux merged commit 8517fe6 into dev Jun 13, 2024
4 checks passed
@jpjarnoux jpjarnoux deleted the manage_chevron_in_GFF branch June 13, 2024 09:02
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants