maaps --fasta examples/Den4_MAAPS_TestData16.fastaMaaps is a program that identifies mixed amino acid positions within an alignment of sequences and where they are located both in terms of nucleotide and amino acid position.
Maaps currently only takes one argument, --fasta. All other arguments are ignored.
Maaps expects a pre-aligned fasta file. Because the sequences are expected to be in a valid reading frame, all sequences must be of length divisible by 3.
Maaps currently does not support gene-coordinate annotations.
Maaps currently only outputs those changes that result in a 'mixed amino acid' at the site in question, it does not report positions where the change is synonymous. In order to report synonymous positions, please use the --syn flag.
While there are no requirements for the fasta headers, any spaces or other white-space characters will be replaced with underscores in the output.
ID Codon NTPos AA AAPos RowType
Den4 TAA - ! 3388 Stop_Codon
Den4 TAG - ! 3414 Stop_Codon
Den4 TAA - ! 3422 Stop_Codon
Den4 TAG - ! 3473 Stop_Codon
2055 TGA - ! 121 Stop_Codon
2055 RAC 1927 N/D 643 Non_Synonymous
Line breaks indicate the start of annotations for a new sequence; sequences are reported in the order they appeared in the input file. If a sequence ID does not appear in the output file, that means no annotations were found for that sequence.
Maaps reports the following annotations:
- Non-synonymous degenerate codons
- Stop codons in the middle of the sequence
- Gaps
- Ns
The following features are planned:
- Gene coordinate support accepting any of the following:
- Genbank ID, genbank file, TSV file
- Report frame shifts
- Integrate stop-codon-checking with gene coordinate information
- Report if the sequence/gene does not end with a stop codon
- Automatic alignment
The following development features are planned:
- Regression tests
- Travis Integration
- hpc reporting
- hlint reporitng
- liquid tags
Run tests:
$ stack exec doctest src