Miniprot boundary scorer

Miniprot boundary scorer parses introns, starts, stops and exons from miniprot's alignment output and scores them. Introns, starts and stops are scored based on local alignment quality around their boundaries. The scoring is similar to ProtHint's scoring of Spaln alignments, described in https://academic.oup.com/nargab/article/2/2/lqaa026/5836691.

Installation and usage

To install, clone this repository and run make in the root folder.

To run, use the following command:

miniprot_boundary_scorer < miniprot_input -o output_file -s matrix_file [optional arguments]

Input details:

• The program can parse multiple separate alignments saved in the same input.
• The input is read from stdin -- can be piped directly from miniprot.

Available options are:

   -o Where to save output file
   -s Path to amino acid scoring matrix
   -w Width of a scoring window around introns. Default = 10
   -k Specify type of weighting kernel used. Available opti-
      ons are "triangular", "box", "parabolic" and 
      "triweight". Triangular kernel is the default option.
   -e Minimum exon score. Exons with lower scores (as wells as int-
      rons bordering such low-scoring exons and starts/stops inside
      them are not printed). Initial exons are treated separately.
      See the options -x and -i for details. Default = 25
   -x Minimum initial exon score. Initial exons with lower scores
      (as well as introns bordering such low-scoring exons and starts
      inside them) are not printed. Initial exons with scores between
      (-e and -x) must also define an initial intron which passes the
      -i filter. Default = 25
   -i Minimum initial intron score. Initial introns bordering
      initial exons with scores < -e that have lower intron scores
      (as well as initial exons bordering such low-scoring
      introns and starts in those exons) are not printed.
      Default = 0
   -g Penalty for gaps, both in exons and around intron boundaries.
      Default = 4
   -f Penalty for frameshifts around exon boundaries. After
      a frameshift is detected, the rest of the exon boundary
      is scored (still using the weighted score) by this penlalty,
      regardless of the actual matches in the alignment.
      Default = 4
   -F Penalty for frameshifts and read-through stop codons in
      exons. Default = 20

Tests

Unit tests are located in the test folder. To compile a test binary, run make test in the root folder. Subsequently, run the test binary to evaluate the tests:

make test
test/t_miniprot_boundary_scorer