Sha256: f28e04d1fc43461ce3e455fbab2e6198044d872d7671b993611990bf36722382
Contents?: true
Size: 1.53 KB
Versions: 9
Compression:
Stored size: 1.53 KB
Contents
# 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/
Version data entries
9 entries across 9 versions & 1 rubygems