changed Seq.new argument to hash

[biopieces.git] / code_ruby / lib / maasha / genbank.rb

diff --git a/code_ruby/lib/maasha/genbank.rb b/code_ruby/lib/maasha/genbank.rb
index dcdfbe32593ec5c883f2ae9036e555ebe3963c52..9635efd69f92971b6cac9ab54c3331885c77ee28 100644 (file)
--- a/code_ruby/lib/maasha/genbank.rb
+++ b/code_ruby/lib/maasha/genbank.rb
@@ -1,4 +1,4 @@
-# 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
@@ -22,6 +22,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+require 'maasha/locator'
 require 'maasha/seq'
 require 'maasha/filesys'
 require 'pp'
@@ -67,7 +68,7 @@ class Genbank < Filesys
 
     block.chomp!("//" + $/ )
 
-    entry = block.split $/
+    entry = block.tr("\r", "\n").split $/
 
     return nil if entry.empty?
 
@@ -80,13 +81,13 @@ class Genbank < Filesys
     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
@@ -146,7 +147,7 @@ class GenbankFeatures
 
   def each
     while @entry[@i] and @entry[@i] !~ /^ORIGIN/
-      if @entry[@i] =~ /^\s{5}([A-Za-z_-]+)/
+      if @entry[@i] =~ /^\s{5}([53'A-Za-z_-]+)/
         if want_feat? $1
           record = {}
 
@@ -154,7 +155,7 @@ class GenbankFeatures
 
           @j = @i + 1
 
-          while @entry[@j] and @entry[@j] !~ /^(\s{21}\/|\s{5}[A-Za-z_-]|[A-Z])/
+          while @entry[@j] and @entry[@j] !~ /^(\s{21}\/|\s{5}[53'A-Za-z_-]|[A-Z])/
             loc << @entry[@j].lstrip
             @j += 1
           end
@@ -180,7 +181,7 @@ class GenbankFeatures
     quals = {}
     k     = 0
 
-    while @entry[@j] and @entry[@j] !~ /^\s{5}[A-Za-z_-]|^[A-Z]/
+    while @entry[@j] and @entry[@j] !~ /^\s{5}[53'A-Za-z_-]|^[A-Z]/
       if @entry[@j] =~ /^\s{21}\/([^=]+)="([^"]+)/
         qual = $1
         val  = $2
@@ -188,7 +189,7 @@ class GenbankFeatures
         if want_qual? qual
           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
@@ -232,130 +233,4 @@ class GenbankFeatures
   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__