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…le calling results.
… only the variable positions.
…positions if there are gaps or ambiguous bases. Remove $ from template commands in docs to allow users to copy and run commands without having to delete the $.
… if any of the sequences has gaps or ambiguous characters. Add option to provide custom options to run MAFFT.
…O.index_db to store record information as a file on disk and to allow using the index with multiprocessing by efficiently loading the index in each process.
… module to compute the loci MSAs.
rfm-targa
added
Type: Enhancement
Status: In Progress
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This PR adds the ComputeMSA module.
The ComputeMSA module computes Multiple Sequence Alignments (MSAs) from allele calling results. It imports a matrix with allelic profiles, creates FASTA files with the alleles identified in each sample per schema locus, and uses MAFFT to compute loci MSAs. The loci MSAs are merged to create wg/cgMLST MSAs. The module can create MSAs at the protein and DNA levels (i.e. by converting the protein MSAs back to DNA). Additionally, it can create MSAs with only the variable positions (SNPs). The default mode expects a TSV file containing allelic profiles, but the module also accepts a path to a directory containing FASTA files to compute a MSA for the sequences in each file.