Class | Bio::Fasta::Report::Hit::Query |
In: |
lib/bio/appl/fasta/format10.rb
|
Parent: | Object |
data | [R] | Returns a Hash containing ‘sq_len’, ‘sq_offset’, ‘sq_type’, ‘al_start’, ‘al_stop’, and ‘al_display_start’ values. You can access most of these values by Report::Hit#query_* methods. |
definition | [R] | Returns the definition of the entry as a String. You can access this value by Report::Hit#query_def method. |
sequence | [R] | Returns the sequence (with gaps) as a String. You can access this value by the Report::Hit#query_seq method. |
# File lib/bio/appl/fasta/format10.rb, line 243 243: def initialize(data) 244: @definition, *data = data.split(/\n/) 245: @data = {} 246: @sequence = '' 247: 248: pat = /;\s+([^:]+):\s+(.*)/ 249: 250: data.each do |x| 251: if pat.match(x) 252: @data[$1] = $2 253: else 254: @sequence += x 255: end 256: end 257: end
Returns the first word in the definition as a String. You can get this value by Report::Hit#query_id method.
# File lib/bio/appl/fasta/format10.rb, line 274 274: def entry_id 275: @definition[/\S+/] 276: end
Returns the sequence length. You can access this value by the Report::Hit#query_len method.
# File lib/bio/appl/fasta/format10.rb, line 280 280: def length 281: @data['sq_len'].to_i 282: end
Returns ‘p’ for protein sequence, ‘D’ for nucleotide sequence.
# File lib/bio/appl/fasta/format10.rb, line 285 285: def moltype 286: @data['sq_type'] 287: end
Returns alignment start position. You can also access this value by Report::Hit#query_start method for shortcut.
# File lib/bio/appl/fasta/format10.rb, line 291 291: def start 292: @data['al_start'].to_i 293: end
Returns alignment end position. You can access this value by Report::Hit#query_end method for shortcut.
# File lib/bio/appl/fasta/format10.rb, line 297 297: def stop 298: @data['al_stop'].to_i 299: end