Output gene sequences to run gene alignment separately

[boasvdp]

Output gene sequences to run gene alignment separately

[SionBayliss]

Hi,

Apologies that I missed this issue, it has been a very busy few months for me. Is this still something that you would like? I would be happy to modify the code for you.

All the best,
Sion

[boasvdp]

Hi, no worries! This would definitely still be useful. I'd be very grateful if you could implement this!

[SionBayliss]

I have just pushed a commit to master with an additional option in align_feature_sequences.pl. You can run align_feature sequences after the PIRATE run has completed. If you need to chunk your data into smaller jobs then simply subset the PIRATE.gene_families.tsv file into separate files, the script will only process/align the genes in the input file (provided with -i). You can switch off alignment using the --align-off (-a) switch.

For example:

PIRATE/scripts/align_feature_sequences.pl -i ./PIRATE.gene_families.tsv -g ./modified_gffs/ -o ./feature_sequences/ -p number_of_thread -d highest_gene_copy_number_to_include(e.g. 1.25) --align-off

I hope that helps,
Sion

[boasvdp]

Great, thanks! I will test it on my data soon, will let you know how it works for me!