Add code skeleton to output sequence of new codon around mutated site#50
Add code skeleton to output sequence of new codon around mutated site#50mmokrejs wants to merge 1 commit into
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…site This roughly sketches places which need to be added to provide codon sequence and their frequency in the output. I never wrote anything in GO so this is an incomplete. The pkg/variants/pairwise.go needs more work to figure out where is the current mutation located in respect to the codon and then slice out the three nucleotides including current position.
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In overall, I am after getting something like I think I would prefer simpler CSV/TSV file format than the default I am surprised that there is no other tool able to parse SAM/BAM or ALN formats and return a list of 64 -item arrays of the codons for every triplet in the alignment columns, properly skipping indels conflicting the supposedly error-free reference (in other words, complying the GFF3 annotation). Respecting an in-frame insertion or deletion in the sample spanning 3 or 6 and so on nucleotides, would be even better but ATM I do not know how to tackle that. Somewhat similar tool is: http://atgme.org/ https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-43 https://academic.oup.com/nar/article/48/19/11030/5921303 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08635-0 https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-023-02230-y https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02966-1 |
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This roughly sketches places which need to be added to provide codon sequence and their frequency in the output. I never wrote anything in GO so this is incomplete. The pkg/variants/pairwise.go needs more work to figure out where is the current mutation located in respect to the codon and then slice out the three nucleotides including current position.