Class Bio::Blat::Report::SegmentPair
In: lib/bio/appl/blat/report.rb  (CVS)
Parent: Object

Sequence segment pair of BLAT result. Similar to Bio::Blast::Report::Hsp but lacks many methods.

Methods

align_len   new  

Attributes

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.

Public Class methods

new(query_len, target_len, strand, blksize, qstart, tstart, qseq, tseq, protein_flag)

Creates a new SegmentPair object. It is designed to be called internally from Bio::Blat::Report class. Users shall not use it directly.

[Source]

# File lib/bio/appl/blat/report.rb, line 158
        def initialize(query_len, target_len, strand,
                       blksize, qstart, tstart, qseq, tseq,
                       protein_flag)
          @blocksize  = blksize
          @qseq       = qseq
          @hseq       = hseq
          @hit_strand   = 'plus'
          w = (protein_flag ? 3 : 1) # 3 means query=protein target=dna
          case strand
          when '-'
            # query is minus strand
            @query_strand = 'minus'
            # convert positions
            @query_from = query_len - qstart
            @query_to   = query_len - qstart - blksize + 1
            # To keep compatibility, with other homology search programs,
            # we add 1 to each position number.
            @hit_from   = tstart + 1
            @hit_to     = tstart + blksize * w # - 1 + 1
          when '+-'
            # hit is minus strand
            @query_strand = 'plus'
            @hit_strand = 'minus'
            # To keep compatibility, with other homology search programs,
            # we add 1 to each position number.
            @query_from   = qstart + 1
            @query_to     = qstart + blksize # - 1 + 1
            # convert positions
            @hit_from     = target_len - tstart
            @hit_to       = target_len - tstart - blksize * w + 1
          else #when '+', '++'
            @query_strand = 'plus'
            # To keep compatibility with other homology search programs,
            # we add 1 to each position number.
            @query_from = qstart + 1
            @query_to   = qstart + blksize # - 1 + 1
            @hit_from   = tstart + 1
            @hit_to     = tstart + blksize * w # - 1 + 1
          end
        end

Public Instance methods

align_len()

Returns alignment length of the segment pair. Returns nil if no alignment data are available.

[Source]

# File lib/bio/appl/blat/report.rb, line 240
        def align_len
          @qseq ? @qseq.size : nil
        end

[Validate]