Class | Bio::Blat::Report::SegmentPair |
In: |
lib/bio/appl/blat/report.rb
|
Parent: | Object |
Sequence segment pair of BLAT result. Similar to Bio::Blast::Report::Hsp but lacks many methods.
blocksize | [R] | Returns block size (length) of the segment pair. This would be a Bio::Blat specific method. |
hit_from | [R] | Returns target (subject, hit) start position. CAUTION: In Blat‘s raw result(psl format), first position is 0. To keep compatibility, the parser add 1 to the position. |
hit_strand | [R] | Returns strand information of the target (subject, hit). Returns ‘plus’ or ‘minus’. |
hit_to | [R] | Returns target (subject, hit) end position. CAUTION: In Blat‘s raw result(psl format), first position is 0. To keep compatibility, the parser add 1 to the position. |
hseq | [R] | Returns the target (subject, hit) sequence. If sequence data is not available, returns nil. |
qseq | [R] | Returns query sequence. If sequence data is not available, returns nil. |
query_from | [R] | Returns query start position. CAUTION: In Blat‘s raw result(psl format), first position is 0. To keep compatibility, the parser add 1 to the position. |
query_strand | [R] | Returns strand information of the query. Returns ‘plus’ or ‘minus’. |
query_to | [R] | Returns query end position. CAUTION: In Blat‘s raw result(psl format), first position is 0. To keep compatibility, the parser add 1 to the position. |
Creates a new SegmentPair object. It is designed to be called internally from Bio::Blat::Report class. Users shall not use it directly.
# File lib/bio/appl/blat/report.rb, line 199 199: def initialize(query_len, target_len, strand, 200: blksize, qstart, tstart, qseq, tseq, 201: protein_flag) 202: @blocksize = blksize 203: @qseq = qseq 204: @hseq = hseq 205: @hit_strand = 'plus' 206: w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna 207: case strand 208: when '-' 209: # query is minus strand 210: @query_strand = 'minus' 211: # convert positions 212: @query_from = query_len - qstart 213: @query_to = query_len - qstart - blksize + 1 214: # To keep compatibility, with other homology search programs, 215: # we add 1 to each position number. 216: @hit_from = tstart + 1 217: @hit_to = tstart + blksize * w # - 1 + 1 218: when '+-' 219: # hit is minus strand 220: @query_strand = 'plus' 221: @hit_strand = 'minus' 222: # To keep compatibility, with other homology search programs, 223: # we add 1 to each position number. 224: @query_from = qstart + 1 225: @query_to = qstart + blksize # - 1 + 1 226: # convert positions 227: @hit_from = target_len - tstart 228: @hit_to = target_len - tstart - blksize * w + 1 229: else #when '+', '++' 230: @query_strand = 'plus' 231: # To keep compatibility with other homology search programs, 232: # we add 1 to each position number. 233: @query_from = qstart + 1 234: @query_to = qstart + blksize # - 1 + 1 235: @hit_from = tstart + 1 236: @hit_to = tstart + blksize * w # - 1 + 1 237: end 238: end