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# Define constants used by SequenceServer module
module SequenceServer
# Define constanst used by BLAST module.
module BLAST
ERROR_LINE = /Error:\s(.*)/
ALGORITHMS = %w(blastn blastp blastx tblastn tblastx)
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(' ')
STDREP = %w(qseqid sseqid sscinames pident length mismatch gapopen qstart qend
sstart send evalue bitscore qcovs qcovhsp).join(' ')
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]
}
end
end
# References
# ----------
# [1]: http://www.ncbi.nlm.nih.gov/books/NBK1763/
Version data entries
8 entries across 8 versions & 1 rubygems