forester/ruby/evoruby/lib/evo/io/parser/ncbi_tseq_parser.rb

   1 #
   2 # = lib/evo/io/parser/ncbi_tseq_parser - NcbiTSeqParser class
   3 #
   4 # Copyright::  Copyright (C) 2006-2007 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: ncbi_tseq_parser.rb,v 1.5 2009/01/07 02:48:20 cmzmasek Exp $
   8
   9
  10 require 'lib/evo/io/parser/msa_parser'
  11 require 'lib/evo/taxonomy/taxonomy'
  12 require 'lib/evo/msa/msa'
  13
  14 require 'iconv'
  15
  16 module Evoruby
  17
  18     class NcbiTSeqParser < MsaParser
  19
  20         TSEQ_SEQ = "TSeq_sequence"
  21         TSEQ_DEFLINE = "TSeq_defline"
  22         TSEQ_ORGNAME = "TSeq_orgname"
  23         TSEQ_TAXID = "TSeq_taxid"
  24         TSEQ_SID = "TSeq_sid"
  25         TSEQ_ACCVER = "TSeq_accver"
  26         TSEQ_GI = "TSeq_gi"
  27         TSEQ_TYPE = "TSeq_seqtype"
  28         TSEQ_LENGTH = "TSeq_length"
  29
  30         def initialize
  31         end
  32
  33
  34         #  <TSeqSet>
  35         #<TSeq>
  36         #  <TSeq_seqtype value="protein"/>
  37         #  <TSeq_gi>29341016</TSeq_gi>
  38         #  <TSeq_accver>AAO78806.1</TSeq_accver>
  39         #  <TSeq_sid>gnl|mbpwusl|BT3701</TSeq_sid>
  40         #  <TSeq_taxid>226186</TSeq_taxid>
  41         #  <TSeq_orgname>Bacteroides thetaiotaomicron VPI-5482</TSeq_orgname>
  42         #  <TSeq_defline>SusD [Bacteroides thetaiotaomicron VPI-5482]</TSeq_defline>
  43         #  <TSeq_length>551</TSeq_length>
  44         #  <TSeq_sequence>MKTKYIKQLFSAALIAVLSSGVTSCINDLDISPIDPQTGGSFDQQGVFVKGYAMLGVTGQKGIDGSPDLDGQDEGESGFYRTTFNCNELPTDECLWAWQENQDIPQLTSISWSPSSQRTEWVYVRLGYDITQYNFFLDQTEGMTDAETLRQRAEIRFLRALHYWYFLDLFGKAPFKEHFSNDLPVEKKGTELYTYIQNELNEIEADMYEPRQAPFGRADKAANWLLRARLYLNAGVYTGQTDYAKAEEYASKVIGSAYKLCTNYSELFMADNDENENAMQEIILPIRQDGVKTRNYGGSTYLVCGTRVAGMPRMGTTNGWSCIFARAAMVQKFFSNLEDVPMLPADVEIPTKGLDTDEQIDAFDAEHGIRTEDMIKAAGDDRALLYSGVGGGRRKIQTDAISGFTDGLSIVKWQNYRSDGKPVSHATYPDTDIPLFRLAEAYLTRAEAIFRQGGDATGDINELRKRANCTRKVQTVTEQELIDEWAREFYLEGRRRSDLVRFGMFTTNKYLWDWKGGAMNGTSVASYYNKYPIPVSDINNNRNMSQNEGYK</TSeq_sequence>
  45         #</TSeq>
  46
  47         def parse( path )
  48             Util.check_file_for_readability( path )
  49             seqs = Msa.new
  50
  51             in_seq        = false
  52             gi = nil
  53             accver = nil
  54             sid = nil
  55             taxid = nil
  56             orgname = nil
  57             defline = nil
  58             seq_str = nil
  59             line_counter = 1
  60             ic = Iconv.new( 'UTF-8//IGNORE', 'UTF-8' )
  61             File.open( path ) do | file |
  62                 while line = file.gets
  63                     line = ic.iconv( line )
  64                     line_counter += 1
  65                     if can_ignore?( line )
  66
  67                     elsif line =~ /^\s*<TSeq>/
  68                         in_seq = true
  69
  70
  71                     elsif in_seq
  72                         if line =~ /^\s*<\/TSeq>/
  73                             in_seq = false
  74                             taxonomy = nil
  75                             if taxid != nil || orgname != nil
  76                                 id_source = nil
  77                                 if taxid != nil
  78                                     id_source = "ncbi"
  79                                 end
  80                                 taxonomy = Taxonomy.new( orgname, taxid , id_source )
  81                             end
  82                             id = nil
  83                             id_source = nil
  84                             symbol = nil
  85                             if gi != nil
  86                                 id = gi
  87                                 id_source = "gi"
  88                                 if sid != nil
  89                                     symbol = sid
  90                                 elsif accver != nil
  91                                     symbol = accver
  92                                 end
  93                             elsif sid != nil
  94                                 id = sid
  95                                 id_source = "ncbi"
  96                                 if accver != nil
  97                                     symbol = accver
  98                                 end
  99                             elsif accver != nil
 100                                 id = accver
 101                                 id_source = "ncbi"
 102                             end
 103
 104                             sequence = Sequence.new( defline,
 105                                 seq_str,
 106                                 id,
 107                                 id_source,
 108                                 taxonomy,
 109                                 symbol )
 110
 111                             seqs.add_sequence( sequence )
 112                             gi = nil
 113                             accver = nil
 114                             sid = nil
 115                             taxid = nil
 116                             orgname = nil
 117                             defline = nil
 118                             seq_str = nil
 119                         elsif line =~ /^\s*<#{TSEQ_GI}>(\d+)<\/#{TSEQ_GI}>/
 120                             gi = $1
 121                         elsif line =~ /^\s*<#{TSEQ_ACCVER}>(.+)<\/#{TSEQ_ACCVER}>/
 122                             accver = $1
 123                         elsif line =~ /^\s*<#{TSEQ_SID}>(.+)<\/#{TSEQ_SID}>/
 124                             sid = $1
 125                         elsif line =~ /^\s*<#{TSEQ_TAXID}>(\d+)<\/#{TSEQ_TAXID}>/
 126                             taxid = $1
 127                         elsif line =~ /^\s*<#{TSEQ_ORGNAME}>(.+)<\/#{TSEQ_ORGNAME}>/
 128                             orgname = $1
 129                         elsif line =~ /^\s*<#{TSEQ_DEFLINE}>(.+)<\/#{TSEQ_DEFLINE}>/
 130                             defline = $1
 131                         elsif line =~ /^\s*<#{TSEQ_SEQ}>(.+)<\/#{TSEQ_SEQ}>/
 132                             seq_str = $1
 133                         elsif line =~ /^\s*<#{TSEQ_TYPE}/
 134                         elsif line =~ /^\s*<#{TSEQ_LENGTH}/
 135                         else
 136                             error_msg = "unexpected line format at line #{line_counter}: " + line
 137                             raise IOError, error_msg
 138                         end
 139                     end
 140                 end
 141             end
 142             return seqs
 143         end
 144
 145         private
 146
 147         def can_ignore?( line )
 148             return ( line !~ /\S/ )
 149         end
 150
 151     end # class NcbiTSeqParser
 152
 153 end # module Evoruby