Rename GFF3 Sequence Names

Question

[pthom010]

I have a GFF3 file that looks like this:

X_Chr1  maker   exon    225515  226772  .   -   .   ID=X-6_Chr1v1_00045.1:13;Parent=X_Chr1v1_00045.1
X_Chr1  maker   exon    227294  227414  .   -   .   ID=X-6_Chr1v1_00045.1:12;Parent=X_Chr1v1_00045.1
X_Chr1  maker   exon    227583  227973  .   -   .   ID=X-6_Chr1v1_00045.1:11;Parent=X_Chr1v1_00045.1
X_Chr1  maker   exon    228164  228232  .   -   .   ID=X-6_Chr1v1_00045.1:10;Parent=X_Chr1v1_00045.1

I would like to take the ID value (ID = X-6_Chr1v10045.1) for each of these genes and make tat the new name of the gene (the first column). Would anybody be able to point me to a package or code that is capable of doing so?

[Ram]

Please edit your post and use an accurate title: You're renaming sequence names in a GFF file and modifying content, not renaming a GFF3 file. The former is a bioinformatics problem, the latter is a computer science basic task.

[Juke34]

AGAT contains a script (agat_sp_manage_IDs.pl) to manage your IDs. I don't know if it can do exactly what you want but it may help you.

Answer 1

[rpolicastro]

You could use sed to do this.

sed -E 's/(^\S+)(.+ID=)([^:]+)(:.+)/\3\2\3\4/' in.gff3 > out.gff3

X-6_Chr1v1_00045.1  maker   exon    225515  226772  .   -   .   ID=X-6_Chr1v1_00045.1:13;Parent=X_Chr1v1_00045.1
X-6_Chr1v1_00045.1  maker   exon    227294  227414  .   -   .   ID=X-6_Chr1v1_00045.1:12;Parent=X_Chr1v1_00045.1
X-6_Chr1v1_00045.1  maker   exon    227583  227973  .   -   .   ID=X-6_Chr1v1_00045.1:11;Parent=X_Chr1v1_00045.1
X-6_Chr1v1_00045.1  maker   exon    228164  228232  .   -   .   ID=X-6_Chr1v1_00045.1:10;Parent=X_Chr1v1_00045.1