[BioRuby-cvs] bioruby/lib/bio/appl/spidey report.rb,1.5,1.6
Naohisa Goto
ngoto at pub.open-bio.org
Mon Oct 31 05:56:16 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/appl/spidey
In directory pub.open-bio.org:/tmp/cvs-serv32078
Modified Files:
report.rb
Log Message:
changed document from RD to RDoc
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/spidey/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb 11 Oct 2005 15:30:01 -0000 1.5
--- report.rb 31 Oct 2005 10:56:14 -0000 1.6
***************
*** 1,7 ****
#
! # bio/appl/spidey/report.rb - SPIDEY result parser
#
! # Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
--- 1,9 ----
#
! # = bio/appl/spidey/report.rb - SPIDEY result parser
#
! # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng at bioruby.org>
! # Licence:: LGPL
#
+ #--
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
***************
*** 17,35 ****
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id$
#
require 'bio'
! module Bio
! class Spidey
class Report #< DB
! #
# File format: -p 0 (default) or -p 1 options
DELIMITER = RS = "\n--SPIDEY "
def initialize(str)
str = str.sub(/\A\s+/, '')
--- 19,59 ----
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ #++
#
# $Id$
#
+ # NCBI Spidey result parser.
+ # Currently, output of default (-p 0 option) or -p 1 option are supported.
+ #
+ # == Notes
+ #
+ # The mRNA sequence is regarded as a query, and
+ # the enomic sequence is regarded as a target (subject, hit).
+ #
+ # == References
+ #
+ # * Wheelan, S.J., et al., Spidey: a tool for mRNA-to-genomic alignments,
+ # Genome Research, 11, 1952--1957, 2001.
+ # http://www.genome.org/cgi/content/abstract/11/11/1952
+ # * http://www.ncbi.nlm.nih.gov/spidey/
+ #
require 'bio'
! module Bio #:nodoc:
! class Spidey #:nodoc:
+ # Spidey report parser class.
+ # Its object may contain some Bio::Spidey::Report::Hit objects.
class Report #< DB
! #--
# File format: -p 0 (default) or -p 1 options
+ #++
+ # Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER = RS = "\n--SPIDEY "
+ # Creates a new Bio::Spidey::Report object from String.
+ # You can use Bio::FlatFile to read a file.
def initialize(str)
str = str.sub(/\A\s+/, '')
***************
*** 46,54 ****
end
end
attr_reader :entry_overrun
- attr_reader :hits, :all_hits
class SeqDesc
# description/definitions of a sequence
def initialize(seqid, seqdef, len)
@entry_id = seqid
--- 70,96 ----
end
end
+ # piece of next entry. Bio::FlatFile uses it.
attr_reader :entry_overrun
+ # Returns an Array of Bio::Spidey::Report::Hit objects.
+ # Because current version of SPIDEY supports only 1 genomic sequences,
+ # the number of hits is 1 or 0.
+ attr_reader :hits
+
+ # Returns an Array of Bio::Spidey::Report::Hit objects.
+ # Unlike Bio::Spidey::Report#hits, the method returns
+ # results of all trials of pairwise alignment.
+ # This would be a Bio::Spidey specific method.
+ attr_reader :all_hits
+
+ # SeqDesc stores sequence information of query or subject.
class SeqDesc
+ #--
# description/definitions of a sequence
+ #++
+
+ # Creates a new SeqDesc object.
+ # It is designed to be called from Bio::Spidey::Report::* classes.
+ # Users shall not call it directly.
def initialize(seqid, seqdef, len)
@entry_id = seqid
***************
*** 56,61 ****
@len = len
end
- attr_reader :entry_id, :definition, :len
def self.parse(str)
/^(Genomic|mRNA)\:\s*(([^\s]*) (.+))\, (\d+) bp\s*$/ =~ str.to_s
--- 98,114 ----
@len = len
end
+ # Identifier of the sequence.
+ attr_reader :entry_id
+
+ # Definition of the sequence.
+ attr_reader :definition
+
+ # Length of the sequence.
+ attr_reader :len
+
+ # Parses piece of Spidey result text and creates a new SeqDesc object.
+ # It is designed to be called from Bio::Spidey::Report::* classes.
+ # Users shall not call it directly.
def self.parse(str)
/^(Genomic|mRNA)\:\s*(([^\s]*) (.+))\, (\d+) bp\s*$/ =~ str.to_s
***************
*** 67,72 ****
end #class SeqDesc
class SegmentPair
! # segment pair (like Bio::BLAST::*::Report::HSP)
def initialize(genomic, mrna, midline, aaseqline,
percent_identity, mismatches, gaps, splice_site,
--- 120,137 ----
end #class SeqDesc
+ # Sequence segment pair of Spidey result.
+ # Similar to Bio::Blast::Report::Hsp but lacks many methods.
+ # For mRNA-genome mapping programs, unlike other homology search
+ # programs, the class is used not only for exons but also for introns.
+ # (Note that intron data would not be available according to run-time
+ # options of the program.)
class SegmentPair
! #--
! # segment pair (like Bio::BLAST::*::Report::Hsp)
! #++
!
! # Creates a new SegmentPair object.
! # It is designed to be called from Bio::Spidey::Report::* classes.
! # Users shall not call it directly.
def initialize(genomic, mrna, midline, aaseqline,
percent_identity, mismatches, gaps, splice_site,
***************
*** 82,89 ****
@align_len = align_len
end
- attr_reader :genomic, :mrna, :midline, :aaseqline,
- :percent_identity, :mismatches, :gaps,
- :splice_site, :align_len
def self.new_intron(from, to, strand, aln)
genomic = Segment.new(from, to, strand, aln[0])
--- 147,194 ----
@align_len = align_len
end
+ # Returns segment informations of the 'Genomic'.
+ # Returns a Bio::Spidey::Report::Segment object.
+ # This would be a Bio::Spidey specific method.
+ attr_reader :genomic
+
+ # Returns segment informations of the 'mRNA'.
+ # Returns a Bio::Spidey::Report::Segment object.
+ # This would be a Bio::Spidey specific method.
+ attr_reader :mrna
+
+ # Returns the middle line of the alignment of the segment pair.
+ # Returns nil if no alignment data are available.
+ attr_reader :midline
+
+ # Returns amino acide sequence in alignment.
+ # Returns String, because white spaces is also important.
+ # Returns nil if no alignment data are available.
+ attr_reader :aaseqline
+
+ # Returns percent identity of the segment pair.
+ attr_reader :percent_identity
+
+ # Returns mismatches.
+ attr_reader :mismatches
+ alias mismatch_count mismatches
+
+ # Returns gaps.
+ attr_reader :gaps
+
+ # Returns splice site information.
+ # Returns a hash which contains :d and :a for keys and
+ # 0, 1, or nil for values.
+ # This would be a Bio::Spidey specific methods.
+ attr_reader :splice_site
+
+ # Returns alignment length of the segment pair.
+ # Returns nil if no alignment data are available.
+ attr_reader :align_len
+
+ # Creates a new SegmentPair object when the segment pair is an intron.
+ # It is designed to be called internally from
+ # Bio::Spidey::Report::* classes.
+ # Users shall not call it directly.
def self.new_intron(from, to, strand, aln)
genomic = Segment.new(from, to, strand, aln[0])
***************
*** 94,98 ****
nil, nil, nil, nil, nil)
end
!
def self.parse(str, strand, complement, aln)
/\AExon\s*\d+(\(\-\))?\:\s*(\d+)\-(\d+)\s*\(gen\)\s+(\d+)\-(\d+)\s*\(mRNA\)\s+id\s*([\d\.]+)\s*\%\s+mismatches\s+(\d+)\s+gaps\s+(\d+)\s+splice site\s*\(d +a\)\s*\:\s*(\d+)\s+(\d+)/ =~ str
--- 199,208 ----
nil, nil, nil, nil, nil)
end
!
! # Parses a piece of Spidey result text and creates a new
! # SegmentPair object.
! # It is designed to be called internally from
! # Bio::Spidey::Report::* classes.
! # Users shall not call it directly.
def self.parse(str, strand, complement, aln)
/\AExon\s*\d+(\(\-\))?\:\s*(\d+)\-(\d+)\s*\(gen\)\s+(\d+)\-(\d+)\s*\(mRNA\)\s+id\s*([\d\.]+)\s*\%\s+mismatches\s+(\d+)\s+gaps\s+(\d+)\s+splice site\s*\(d +a\)\s*\:\s*(\d+)\s+(\d+)/ =~ str
***************
*** 121,139 ****
end
# Bio::BLAST::*::Report::Hsp compatible methods
# Methods already defined: midline, percent_identity,
! # gaps, align_len
! alias mismatch_count mismatches
def query_from; @mrna.from; end
def query_to; @mrna.to; end
def qseq; @mrna.seq; end
def query_strand; @mrna.strand; end
def hit_from; @genomic.from; end
def hit_to; @genomic.to; end
def hseq; @genomic.seq; end
def hit_strand; @genomic.strand; end
end #class SegmentPair
class Segment
def initialize(pos_st, pos_ed, strand = nil, seq = nil)
@from = pos_st ? pos_st.to_i : nil
--- 231,275 ----
end
+ #--
# Bio::BLAST::*::Report::Hsp compatible methods
# Methods already defined: midline, percent_identity,
! # gaps, align_len, mismatch_count
! #++
!
! # Returns start position of the mRNA (query) (the first position is 1).
def query_from; @mrna.from; end
+
+ # Returns end position (including its position) of the mRNA (query).
def query_to; @mrna.to; end
+
+ # Returns the sequence (with gaps) of the mRNA (query).
def qseq; @mrna.seq; end
+
+ # Returns strand information of the mRNA (query).
+ # Returns 'plus', 'minus', or nil.
def query_strand; @mrna.strand; end
+
+ # Returns start position of the genomic (target, hit)
+ # (the first position is 1).
def hit_from; @genomic.from; end
+
+ # Returns end position (including its position) of the
+ # genomic (target, hit).
def hit_to; @genomic.to; end
+
+ # Returns the sequence (with gaps) of the genomic (target, hit).
def hseq; @genomic.seq; end
+
+ # Returns strand information of the genomic (target, hit).
+ # Returns 'plus', 'minus', or nil.
def hit_strand; @genomic.strand; end
end #class SegmentPair
+ # Segment informations of a segment pair.
class Segment
+ # Creates a new Segment object.
+ # It is designed to be called internally from
+ # Bio::Spidey::Report::* classes.
+ # Users shall not call it directly.
def initialize(pos_st, pos_ed, strand = nil, seq = nil)
@from = pos_st ? pos_st.to_i : nil
***************
*** 142,149 ****
@seq = seq
end
! attr_reader :from, :to, :strand, :seq
end #class Segment
class Hit
def initialize(data, d0)
@data = data
--- 278,302 ----
@seq = seq
end
!
! # start position
! attr_reader :from
!
! # end position
! attr_reader :to
!
! # strand information
! attr_reader :strand
!
! # sequence data
! attr_reader :seq
end #class Segment
+ # Hit object of Spidey result.
+ # Similar to Bio::Blast::Report::Hit but lacks many methods.
class Hit
+ # Creates a new Hit object.
+ # It is designed to be called internally from
+ # Bio::Spidey::Report::* classes.
+ # Users shall not call it directly.
def initialize(data, d0)
@data = data
***************
*** 151,154 ****
--- 304,308 ----
end
+ # Fetches fields.
def field_fetch(t, ary)
reg = Regexp.new(/^#{Regexp.escape(t)}\:\s*(.+)\s*$/)
***************
*** 161,164 ****
--- 315,319 ----
private :field_fetch
+ # Parses information about strand.
def parse_strand
x = field_fetch('Strand', @d0)
***************
*** 173,176 ****
--- 328,334 ----
private :parse_strand
+ # Returns strand information of the hit.
+ # Returns 'plus', 'minus', or nil.
+ # This would be a Bio::Spidey specific method.
def strand
unless defined?(@strand); parse_strand; end
***************
*** 178,181 ****
--- 336,342 ----
end
+ # Returns true if the result reports 'Reverse complement'.
+ # Otherwise, return false or nil.
+ # This would be a Bio::Spidey specific method.
def complement?
unless defined?(@complement); parse_strand; end
***************
*** 183,186 ****
--- 344,348 ----
end
+ # Returns number of exons in the hit.
def number_of_exons
unless defined?(@number_of_exons)
***************
*** 190,193 ****
--- 352,356 ----
end
+ # Returns number of splice sites of the hit.
def number_of_splice_sites
unless defined?(@number_of_splice_sites)
***************
*** 198,201 ****
--- 361,365 ----
end
+ # Returns overall percent identity of the hit.
def percent_identity
unless defined?(@percent_identity)
***************
*** 207,210 ****
--- 371,375 ----
end
+ # Returns missing mRNA ends of the hit.
def missing_mrna_ends
unless defined?(@missing_mrna_ends)
***************
*** 214,217 ****
--- 379,385 ----
end
+ # Returns sequence informations of the 'Genomic'.
+ # Returns a Bio::Spidey::Report::SeqDesc object.
+ # This would be a Bio::Spidey specific method.
def genomic
unless defined?(@genomic)
***************
*** 221,224 ****
--- 389,395 ----
end
+ # Returns sequence informations of the mRNA.
+ # Returns a Bio::Spidey::Report::SeqDesc object.
+ # This would be a Bio::Spidey specific method.
def mrna
unless defined?(@mrna)
***************
*** 228,231 ****
--- 399,403 ----
end
+ # Parses segment pairs.
def parse_segmentpairs
aln = self.align.dup
***************
*** 271,275 ****
end
private :parse_segmentpairs
!
def exons
unless defined?(@exons); parse_segmentpairs; end
--- 443,449 ----
end
private :parse_segmentpairs
!
! # Returns exons of the hit.
! # Returns an array of Bio::Spidey::Report::SegmentPair object.
def exons
unless defined?(@exons); parse_segmentpairs; end
***************
*** 277,280 ****
--- 451,459 ----
end
+ # Returns introns of the hit.
+ # Some of them would contain untranscribed regions.
+ # Returns an array of Bio::Spidey::Report::SegmentPair objects.
+ # (Note that intron data is not always available
+ # according to run-time options of the program.)
def introns
unless defined?(@introns); parse_segmentpairs; end
***************
*** 282,285 ****
--- 461,469 ----
end
+ # Returns segment pairs (exons and introns) of the hit.
+ # Each segment pair is a Bio::Spidey::Report::SegmentPair object.
+ # Returns an array of Bio::Spidey::Report::SegmentPair objects.
+ # (Note that intron data is not always available
+ # according to run-time options of the program.)
def segmentpairs
unless defined?(@segmentparis); parse_segmentpairs; end
***************
*** 287,290 ****
--- 471,477 ----
end
+ # Returns alignments.
+ # Returns an Array of arrays.
+ # This would be a Bio::Spidey specific method.
def align
unless defined?(@align); parse_align; end
***************
*** 292,295 ****
--- 479,483 ----
end
+ # Parses alignment lines.
def parse_align_lines(data)
misc = [ [], [], [], [] ]
***************
*** 328,331 ****
--- 516,520 ----
private :parse_align_lines
+ # Parses alignments.
def parse_align
r = []
***************
*** 342,352 ****
--- 531,557 ----
private :parse_align
+ #--
# Bio::BLAST::*::Report::Hit compatible methods
+ #++
+
+ # Length of the mRNA (query) sequence.
+ # Same as Bio::Spidey::Report#query_len.
def query_len; mrna.len; end
+
+ # Identifier of the mRNA (query).
+ # Same as Bio::Spidey::Report#query_id.
def query_id; mrna.entry_id; end
+
+ # Definition of the mRNA (query).
+ # Same as Bio::Spidey::Report#query_def.
def query_def; mrna.definition; end
+ # The genomic (target) sequence length.
def target_len; genomic.len; end
+
+ # Identifier of the genomic (target) sequence.
def target_id; genomic.entry_id; end
+
+ # Definition of the genomic (target) sequence.
def target_def; genomic.definition; end
***************
*** 356,370 ****
alias hsps exons
! def each(&x); exons.each(&x); end
end #class Hit
def mrna; @hit.mrna; end
#Bio::BLAST::*::Report compatible methods
def num_hits; @hits.size; end
! def each_hit(&x); @hits.each(&x); end
alias each each_hit
def query_def; @hit.mrna.definition; end
def query_id; @hit.mrna.entry_id; end
def query_len; @hit.mrna.len; end
end #class Report
--- 561,600 ----
alias hsps exons
!
! # Iterates over each exon of the hit.
! # Yields Bio::Spidey::Report::SegmentPair object.
! def each(&x) #:yields: segmentpair
! exons.each(&x)
! end
end #class Hit
+ # Returns sequence informationsof the mRNA.
+ # Returns a Bio::Spidey::Report::SeqDesc object.
+ # This would be a Bio::Spidey specific method.
def mrna; @hit.mrna; end
+ #--
#Bio::BLAST::*::Report compatible methods
+ #++
+
+ # Returns number of hits.
+ # Same as hits.size.
def num_hits; @hits.size; end
!
! # Iterates over each hits.
! # Same as hits.each.
! # Yields a Bio::Spidey::Report::Hit object.
! def each_hit(&x) #:yields: hit
! @hits.each(&x)
! end
alias each each_hit
+
+ # Returns definition of the mRNA (query) sequence.
def query_def; @hit.mrna.definition; end
+
+ # Returns identifier of the mRNA (query) sequence.
def query_id; @hit.mrna.entry_id; end
+
+ # Returns the length of the mRNA (query) sequence.
def query_len; @hit.mrna.len; end
end #class Report
***************
*** 373,605 ****
end #module Bio
- =begin
-
- = Bio::Spidey::Report
-
- --- Bio::Spidey::Report.new(text)
-
- Creates new Bio::Spidey::Report object from String.
- You can use Bio::FlatFile to read a file.
-
- Currently, result created with options -p 0 (default) or -p 1
- are supported.
-
- Note that "mRNA" is always regarded as "query" and
- "Genomic" is always regarded as "subject"(target, hit).
-
- --- Bio::Spidey::Report#hits
-
- Returns an Array of Bio::Spidey::Report::Hit objects.
- Because current version of SPIDEY supports only 1 genomic sequences,
- the number of hits is 1 or 0.
-
- --- Bio::Spidey::Report#all_hits
-
- Returns an Array of Bio::Spidey::Report::Hit objects.
- Unlike Bio::Spidey::Report#hits, the method returns
- results of all trials of pairwise alignment.
- This would be a Bio::Spidey specific method.
-
- --- Bio::Spidey::Report#each_hit
- --- Bio::Spidey::Report#each
-
- Iterates over each Bio::Spidey::Report::Hit object.
- Same as hits.each.
-
- --- Bio::Spidey::Report#num_hits
-
- Returns number of hits.
- Same as hits.size.
-
- --- Bio::Spidey::Report#query_id
-
- Returns the identifier of query sequence.
-
- --- Bio::Spidey::Report#query_def
-
- Returns the definition of query sequence.
-
- --- Bio::Spidey::Report#query_len
-
- Returns the length of query sequence.
-
- --- Bio::Spidey::Report#mrna
-
- Returns sequence informations of "mRNA".
- Returns a Bio::Spidey::Report::SeqDesc object.
- This would be a Bio::Spidey specific method.
-
- == Bio::Spidey::Report::Hit
-
- Hit object of SPIDEY result.
- Similar to Bio::Blast::Report::Hit but lacks many methods.
-
- --- Bio::Spidey::Report::Hit#hit_id
- --- Bio::Spidey::Report::Hit#target_id
-
- Returns the identifier of subject sequence.
-
- --- Bio::Spidey::Report::Hit#definition
- --- Bio::Spidey::Report::Hit#target_def
-
- Returns the identifier of subject sequence.
-
- --- Bio::Spidey::Report::Hit#len
- --- Bio::Spidey::Report::Hit#target_len
-
- Returns the length of subject sequence.
-
- --- Bio::Spidey::Report::Hit#query_id
- --- Bio::Spidey::Report::Hit#query_def
- --- Bio::Spidey::Report::Hit#query_len
-
- Same as Bio::Spidey::Report#(query_id|query_def|query_len).
-
- --- Bio::Spidey::Report::Hit#exons
-
- Returns exons of the hit.
- Each exon is a Bio::Spidey::Report::SegmentPair object.
-
- --- Bio::Spidey::Report::Hit#hsps
-
- Same as Bio::Spidey::Report#exons
- The method aims to provide compatibility between
- other homology search program's result objects.
-
- --- Bio::Spidey::Report::Hit#each
-
- Iterates over each exon (Bio::Spidey::Report::SegmentPair object)
- of the hit.
-
- --- Bio::Spidey::Report::Hit#segmentpairs
-
- Returns segment pairs (exons and introns) of the hit.
- Each segment pair is a Bio::Spidey::Report::SegmentPair object.
- Returns an array of Bio::Spidey::Report::SegmentPair objects.
- (Note that intron data is not always available
- according to run-time options of the program.)
-
- --- Bio::Spidey::Report::Hit#introns
-
- Returns introns of the hit.
- Some of them would contain untranscribed regions.
- Returns an array of Bio::Spidey::Report::SegmentPair objects.
- (Note that intron data is not always available
- according to run-time options of the program.)
-
- --- Bio::Spidey::Report::Hit#mrna
- --- Bio::Spidey::Report::Hit#genomic
-
- Returns sequence informations of "mRNA" or "Genomic", respectively.
- Returns a Bio::Spidey::Report::SeqDesc object.
- These would be Bio::Spidey specific methods.
-
- --- Bio::Spidey::Report::Hit#strand
-
- Returns strand information of the hit.
- Returns 'plus', 'minus', or nil.
- This would be a Bio::Spidey specific method.
-
- --- Bio::Spidey::Report::Hit#complement?
-
- Returns true if the result reports 'Reverse complement'.
- Otherwise, return false or nil.
- This would be a Bio::Spidey specific method.
-
- --- Bio::Spidey::Report::Hit#align
-
- Returns alignments.
- Returns an Array of arrays.
- This would be a Bio::Spidey specific method.
-
- == Bio::Spidey::Report::SegmentPair
-
- Sequence segment pair of SPIDEY result.
- Similar to Bio::Blast::Report::HSP but lacks many methods.
- For mRNA-genome mapping programs, unlike other homology search programs,
- the class is used not only for exons but also for introns.
- (Note that intron data would not be available according to run-time
- options of the program.)
-
- --- Bio::Spidey::Report::SegmentPair#query_from
- --- Bio::Spidey::Report::SegmentPair#query_to
- --- Bio::Spidey::Report::SegmentPair#qseq
-
- --- Bio::Spidey::Report::SegmentPair#hit_from
- --- Bio::Spidey::Report::SegmentPair#hit_to
- --- Bio::Spidey::Report::SegmentPair#hseq
-
- --- Bio::Spidey::Report::SegmentPair#query_strand
- --- Bio::Spidey::Report::SegmentPair#hit_strand
-
- Returns strand information of query or hit, respectively.
- Returns 'plus', 'minus', or nil.
-
- --- Bio::Spidey::Report::SegmentPair#gaps
-
- Returns gaps.
-
- --- Bio::Spidey::Report::SegmentPair#mismatches
- --- Bio::Spidey::Report::SegmentPair#mismatch_count
-
- Returns mismatches.
-
- --- Bio::Spidey::Report::SegmentPair#midline
-
- Returns the "midline" of the segment pair.
- Returns nil if no alignment data are available.
-
- --- Bio::Spidey::Report::SegmentPair#percent_identity
-
- Returns percent identity of the segment pair.
-
- --- Bio::Spidey::Report::SegmentPair#align_len
-
- Returns alignment length of the segment pair.
- Returns nil if no alignment data are available.
-
- --- Bio::Spidey::Report::SegmentPair#aaseqline
-
- Returns amino acide sequence in alignment.
- Returns String, because white spaces in the result is also important.
- Returns nil if no alignment data are available.
- This would be a Bio::Spidey specific methods.
-
- --- Bio::Spidey::Report::SegmentPair#splice_site
-
- Returns splice site information.
- Returns a hash which contains :d and :a for keys and
- 0, 1, or nil for values.
- This would be a Bio::Spidey specific methods.
-
- --- Bio::Spidey::Report::SegmentPair#mrna
- --- Bio::Spidey::Report::SegmentPair#genomic
-
- Returns segment informations of 'mRNA' or 'Genomic', respectively.
- Returns a Bio::Spidey::Report::Segment object.
- These would be Bio::Spidey specific methods.
-
- == Bio::Spidey::Report::Segment
-
- Segment informations of a segment pair.
-
- --- Bio::Spidey::Report::Segment#from
- --- Bio::Spidey::Report::Segment#to
- --- Bio::Spidey::Report::Segment#seq
- --- Bio::Spidey::Report::Segment#strand
-
- == Bio::Spidey::Report::SeqDesc
-
- Sequence information of query or subject.
-
- --- Bio::Spidey::Report::SeqDesc#entry_id
- --- Bio::Spidey::Report::SeqDesc#definition
- --- Bio::Spidey::Report::SeqDesc#len
-
- = References
-
- * ((<URL:http://www.genome.org/cgi/content/abstract/11/11/1952>))
- Wheelan, S.J., et al., Spidey: a tool for mRNA-to-genomic alignments,
- Genome Research, 11, 1952--1957, 2001.
-
- =end
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