Comments (4)
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
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Hi, no worries! This would definitely still be useful. I'd be very grateful if you could implement this!
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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
from pirate.
Great, thanks! I will test it on my data soon, will let you know how it works for me!
from pirate.
Related Issues (20)
- error observed during "aligning all feature sequences" HOT 2
- Missing genome in output HOT 12
- PIRATE_plots.pdf created by plot_summary.R HOT 1
- Error after MCL clustering step HOT 5
- How do you tell which gene families are single-copy or multi-copy? HOT 2
- Feature request: Option to include original IDs and annotations in fasta headers for align_features_sequences script HOT 2
- Average_dose =1 is appropriate to determine whether a gene family is a single copy? HOT 1
- - ERROR: link_clusters.pl failed. HOT 1
- Undefined subroutine &main::translate called HOT 2
- Error when running PIRATE MCL process
- For some single loci, a gene family but for others not. HOT 1
- problem in installation HOT 9
- Bump version in new release HOT 4
- Missing output files and coregenom files HOT 3
- Running on large dataset HOT 2
- stuck at threshold 60 during MCL clustering HOT 3
- PIRATE.pangenome_summary.txt HOT 6
- understanding pirate results
- question on presente/absence gene table data
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