yannickwurm/sequenceserver

# Define constants used by SequenceServer module
module SequenceServer
  # Define constanst used by BLAST module.
  module BLAST
    ERROR_LINE = /Error:\s(.*)/i

    ALGORITHMS = %w[blastn blastp blastx tblastn tblastx].freeze

    OUTFMT_SPECIFIERS = %w[qseqid qgi qacc sseqid sallseqid sgi sallgi sacc
                           sallacc qstart qend sstart send qseq sseq evalue
                           bitscore score length length pident nident
                           mismatch positive gapopen gaps ppos frames
                           qframe hframe btop staxids sscinames scomnames
                           sblastnames sskingdoms stitle salltitles sstrand
                           qcovs qcovhsp].join(' ').freeze

    STDREP = %w[qseqid sseqid sscinames pident length mismatch gapopen qstart
                qend sstart send evalue bitscore qcovs qcovhsp].join(' ').freeze
    OUTFMT = {
      'pairwise'        => [0, :txt],
      'qa'              => [1, :txt],
      'qa_no_identity'  => [2, :txt],
      'fqa'             => [3, :txt],
      'fqa_no_identity' => [4, :txt],
      'xml'             => [5, :xml],
      'std_tsv'         => [7, :tsv, STDREP],
      'full_tsv'        => [7, :tsv, OUTFMT_SPECIFIERS],
      'custom_tsv'      => [7, :tsv, 'qseqid sseqid sscinames qcovs qcovhsp'],
      'asn_text'        => [8, :asn],
      'asn_binary'      => [9, :asn],
      'csv'             => [10, :csv],
      'archive'         => [11, :txt]
    }.freeze
  end
end

# References
# ----------
# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/