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Toggle renaming of gene names in alleles in --change-gene-id #2830

Closed jseager7 closed 2 weeks ago

jseager7 commented 2 weeks ago

I've added a flag --no-rename to canto_admin.pl that, when set with --change-gene-id, skips the renaming of gene names in allele names. This was needed because PHI-base wanted to keep using the gene name that was specified in the publication for our annotations.

The --no-rename flag defaults to 0 instead of undef. If the --no-rename flag is set with any other flag, the script warns and exits:

Error: --no-rename is only allowed with --change-gene-id

This required adding an argument $no_rename to change_gene_id in TrackUtil.pm that skips the allele renaming when set. I didn't bother to set a default value for this argument because change_gene_id is currently only used in one place.

I've tested this with PHI-Canto where it works fine both with and without the new flag. I haven't tested any other modes.

kimrutherford commented 2 weeks ago

Thanks James. Both of those patches look great.