Class | Bio::Blast::WU::Report |
In: |
lib/bio/appl/blast/wublast.rb
|
Parent: | Default::Report |
Bio::Blast::WU::Report parses WU-BLAST default output and stores information in the data. It may contain a Bio::Blast::WU::Report::Iteration object. Because it inherits Bio::Blast::Default::Report, please also refer Bio::Blast::Default::Report.
Returns the name (filename or title) of the database.
# File lib/bio/appl/blast/wublast.rb, line 122 122: def db 123: unless defined?(@db) 124: if /Database *\: *(.*)/m =~ @f0database then 125: a = $1.split(/^/) 126: if a.size > 1 and /\ASearching\..+ done\s*\z/ =~ a[-1] then 127: a.pop 128: end 129: if a.size > 1 and /\A +[\d\,]+ +sequences\; +[\d\,]+ total +letters\.?\s*\z/ =~ a[-1] then 130: a.pop 131: end 132: @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ') 133: end 134: end #unless 135: @db 136: end
(WU-BLAST) Returns exit code for the execution. Returns an Integer or nil.
# File lib/bio/appl/blast/wublast.rb, line 79 79: def exit_code 80: if defined? @exit_code then 81: @exit_code 82: else 83: nil 84: end 85: end
(WU-BLAST) Returns the message bundled with the exit code output. The message will be shown when WU-BLAST ignores a fatal error due to the command line option "-nonnegok", "-novalidctxok", or "-shortqueryok".
Returns a String or nil.
# File lib/bio/appl/blast/wublast.rb, line 93 93: def exit_code_message 94: if defined? @exit_code_message then 95: @exit_code_message 96: else 97: nil 98: end 99: end
Returns e-value threshold specified when BLAST was executed.
# File lib/bio/appl/blast/wublast.rb, line 50 50: def expect; parse_parameters; @parameters['E']; end
Returns parameter matrix (???)
# File lib/bio/appl/blast/wublast.rb, line 44 44: def parameter_matrix 45: parse_parameters 46: @parameter_matrix 47: end
Returns parameters (???)
# File lib/bio/appl/blast/wublast.rb, line 38 38: def parameters 39: parse_parameters 40: @parameters 41: end
(WU-BLAST) Returns record number of the query. It may only be available for reports with multiple queries. Returns an Integer or nil.
# File lib/bio/appl/blast/wublast.rb, line 72 72: def query_record_number 73: format0_parse_query 74: @query_record_number 75: end