Module: SequenceServer::BLAST
- Defined in:
- lib/sequenceserver/blast/hit.rb,
lib/sequenceserver/blast/hsp.rb,
lib/sequenceserver/blast/job.rb,
lib/sequenceserver/blast/error.rb,
lib/sequenceserver/blast/query.rb,
lib/sequenceserver/blast/report.rb,
lib/sequenceserver/blast/constants.rb,
lib/sequenceserver/blast/formatter.rb
Overview
Define constanst used by BLAST module.
Defined Under Namespace
Classes: Error, Formatter, HSP, Hit, Job, Query, Report
Constant Summary collapse
- 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