-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2011 Martin A. Hansen.
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+require 'maasha/locator'
require 'maasha/seq'
require 'maasha/filesys'
+require 'pp'
# Error class for all exceptions to do with Genbank.
class GenbankError < StandardError; end
block.chomp!("//" + $/ )
- entry = block.split $/
+ entry = block.tr("\r", "\n").split $/
return nil if entry.empty?
i = @entry.size
j = i - 1
- while @entry[j] and @entry[j] !~ /^[A-Z]/
+ while @entry[j] and @entry[j] =~ /^\s+\d/
j -= 1
end
seq = @entry[j + 1 .. i].join.delete(" 0123456789")
- Seq.new(nil, seq, "dna") if seq
+ Seq.new(seq: seq, type: :dna) if seq
end
# Method to get the base keys from Genbank entry and return these
end
class GenbankFeatures
- @@i = 0
- @@j = 0
-
def initialize(entry, hash_feats, hash_quals)
@entry = entry
@hash_feats = hash_feats
@hash_quals = hash_quals
+ @i = 0
+ @j = 0
end
def each
- while @entry[@@i] and @entry[@@i] !~ /^ORIGIN/
- if @entry[@@i] =~ /^\s{5}([A-Za-z_-]+)/
+ while @entry[@i] and @entry[@i] !~ /^ORIGIN/
+ if @entry[@i] =~ /^\s{5}([53'A-Za-z_-]+)/
if want_feat? $1
record = {}
- feat, loc = @entry[@@i].lstrip.split(/\s+/, 2)
+ feat, loc = @entry[@i].lstrip.split(/\s+/, 2)
- @@j = @@i + 1
+ @j = @i + 1
- while @entry[@@j] and @entry[@@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
- loc << @entry[@@j].lstrip
- @@j += 1
+ while @entry[@j] and @entry[@j] !~ /^(\s{21}\/|\s{5}[53'A-Za-z_-]|[A-Z])/
+ loc << @entry[@j].lstrip
+ @j += 1
end
get_quals.each_pair { |k,v|
end
end
- @@j > @@i ? @@i = @@j : @@i += 1
+ @j > @i ? @i = @j : @i += 1
end
end
quals = {}
k = 0
- while @entry[@@j] and @entry[@@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
- if @entry[@@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
+ while @entry[@j] and @entry[@j] !~ /^\s{5}[53'A-Za-z_-]|^[A-Z]/
+ if @entry[@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
qual = $1
val = $2
if want_qual? qual
- k = @@j + 1
+ k = @j + 1
- while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+ while @entry[k] and @entry[k] !~ /^(\s{21}\/|\s{5}[53'A-Za-z_-]|[A-Z])/
val << @entry[k].lstrip.chomp('"')
k += 1
end
end
end
- k > @@j ? @@j = k : @@j += 1
+ k > @j ? @j = k : @j += 1
end
quals
end
end
-
-# Error class for all exceptions to do with Genbank/EMBL/DDBJ feature table locators.
-class LocatorError < StandardError; end
-
-class Locator
- attr_accessor :locator, :seq, :subseq
-
- def initialize(locator, seq)
- @locator = locator
- @seq = seq
- @subseq = Seq.new(nil, "", "dna")
- parse_locator(locator)
- end
-
- def strand
- if @locator.match("complement")
- return "-"
- else
- return "+"
- end
- end
-
- def s_beg
- if @locator =~ /(\d+)/
- return $1.to_i - 1
- end
- end
-
- def s_end
- if @locator.reverse =~ /(\d+)/
- return $1.reverse.to_i - 1
- end
- end
-
- private
-
- # Method that uses recursion to parse a locator string from a feature
- # table and fetches the appropriate subsequence. the operators
- # join(), complement(), and order() are handled.
- # the locator string is broken into a comma separated lists, and
- # modified if the parens donnot balance. otherwise the comma separated
- # list of ranges are stripped from operators, and the subsequence are
- # fetched and handled according to the operators.
- # SNP locators are also dealt with (single positions).
- def parse_locator(locator, join = nil, comp = nil, order = nil)
- intervals = locator.split(",")
-
- unless balance_parens?(intervals.first) # locator includes a join/comp/order of several ranges
- case locator
- when /^join\((.*)\)$/
- locator = $1
- join = true
- when /^complement\((.*)\)$/
- locator = $1
- comp = true
- when /^order\((.*)\)$/
- locator = $1
- order = true
- end
-
- parse_locator(locator, join, comp, order)
- else
- intervals.each do |interval|
- case interval
- when /^join\((.*)\)$/
- locator = $1
- join = true
- parse_locator(locator, join, comp, order)
- when /^complement\((.*)\)$/
- locator = $1
- comp = true
- parse_locator(locator, join, comp, order)
- when /^order\((.*)\)$/
- locator = $1
- order = true
- parse_locator(locator, join, comp, order)
- when /^[<>]?(\d+)[^\d]+(\d+)$/
- int_beg = $1.to_i - 1
- int_end = $2.to_i - 1
-
- newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
-
- unless newseq.seq.nil?
- newseq.revcomp if comp
-
- @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
- end
- when /^(\d+)$/
- pos = $1.to_i - 1
-
- newseq = Seq.new(nil, @seq.seq[pos], "dna")
-
- unless newseq.seq.nil?
- newseq.revcomp if comp
-
- @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
- end
- else
- $stderr.puts "WARNING: Could not match locator -> #{locator}";
- @subseq.seq << ""
- end
- end
- end
-
- return @subseq
- end
-
- def balance_parens?(locator)
- parens = 0
-
- locator.each_char do |char|
- case char
- when '(' then parens += 1
- when ')' then parens -= 1
- end
- end
-
- if parens == 0
- return true
- else
- return false
- end
- end
-end
-
-
__END__
projects / biopieces.git / blobdiff