Feat marker genes #31
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Added the ability to print a FASTA file (amino acid) that includes the sequences of the genes that were identified as marker genes in each bin. Feature is implemented in the qa subprogram as a new output format (number 10). Each sequence is printed with an informative header that takes the form: >$bin_id $contig_name geneId=$gene_num;start=$start;end=$end;strand=$strand marker=$marker;mstart=$mstart;mend=$mend Where $ denotes a variable. Variables: - bin_id: FASTA bin the sequence comes from - contig_name: contig the sequence comes from - gene_num: gene number as assigned by Prodigal - start: gene start position on contig (nucleotide) - end: gene end position on contig (nucleotide) - strand: strand the gene is on, 1 or -1 - marker: name of the marker that was identified as a match to the gene - mstart: start position on gene of alignment with marker (amino acid) - mend: end position on gene of alignment with marker (amino acid)
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Thanks Cameron, I have added this to the main branch. I hope to release a new version of CheckM in the next few weeks. I've also added you as a contributor on the CheckM wiki. I very much appreciate the contribution. Cheers, |
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Sounds good! |
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This is an addition that my lab wanted because we wanted to be able to BLAST genes from our bins that were identified as marker genes.
It looks similar to what I think issue #22 is requesting. With that in mind, I thought I'd upload my code. Feel free pull it into the main branch if this is what you had in mind. It would be possible to sort the genes by contig and position on contig to have an ordered FASTA of marker genes. This isn't currently done for speed reasons but it could be a good complement to a graphic of the dispersion of marker genes across the contigs. My lab also has interest in knowing how evenly dispersed the markers are over the genome bin (to ensure we haven't just happened to assemble a region that is dense in markers which makes it look more complete than it actually is). So, I may work on making a dispersion graphic at some time in the future.
Commit 8ee5f90 message describes the addition in more detail.