MAAPs

Usage

maaps --fasta examples/Den4_MAAPS_TestData16.fasta

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.

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.

Features

Maaps reports the following annotations:

• Non-synonymous degenerate codons
• Stop codons in the middle of the sequence
• Gaps
• Ns

Planned Features

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

Development

Run tests:

$ stack exec doctest src