Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script about pirate HOT 2 CLOSED

Hi Alex,

You can rename locus tags/IDs to their original values using the following script:

/tools/subsample/subsample_outputs.pl -i PIRATE.gene_families.ordered.tsv -o PIRATE.gene_families.ordered.renamed.tsv --field "prev_locus"

It won't transfer annotation to alignments but will give you an easy way of looking up/converting your previous locus tags and/or may form a basis of a script to do so.

All the best,
Sion

from pirate.

Dear Sion,

Thank you. I have modified the align_feature_sequences.pl script to include an option for printing additional information to the headers of the fasta alignments. When using the "--full-annot" option, the output looks something like this:

>Rhizobium_jaguaris_CCGE525_00216 prev_ID:CCGE525_35950 prev_locus:CCGE525_35950 genome:Rhizobium_jaguaris_CCGE525 gene:ehuB protein_id:AYG64154.1 product:ectoine/hydroxyectoine ABC transporter substrate-binding protein EhuB

I've attached that modified script to this message: align_feature_sequences_mod.pl.gz

As an aside, I have found that NCBI gff files largely work correctly in PIRATE if I first run them through the AGAT (https://github.com/NBISweden/AGAT) script "agat_convert_sp_gxf2gxf.pl" and then manually add the ##FASTA block to the end of the file. This way I can include the original locus tags and annotation from NCBI without reannotating them in prokka.

Best,
Alex

from pirate.