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

   1 #
   2 # = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class
   3 #
   4 # Copyright::  Copyright (C) 2012 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id:  $
   8
   9
  10 require 'lib/evo/util/constants'
  11 require 'lib/evo/msa/msa_factory'
  12 require 'lib/evo/io/msa_io'
  13 require 'lib/evo/io/writer/fasta_writer'
  14 require 'lib/evo/io/parser/fasta_parser'
  15
  16
  17 module Evoruby
  18
  19   class HmmscanDomainExtractor
  20
  21     TRIM_BY = 2
  22
  23     def initialize
  24     end
  25
  26     # raises ArgumentError, IOError, StandardError
  27     def parse( domain_id,
  28         hmmsearch_output,
  29         fasta_sequence_file,
  30         outfile,
  31         passed_seqs_outfile,
  32         failed_seqs_outfile,
  33         e_value_threshold,
  34         length_threshold,
  35         add_position,
  36         add_domain_number,
  37         add_domain_number_as_digit,
  38         add_domain_number_as_letter,
  39         trim_name,
  40         log )
  41
  42       Util.check_file_for_readability( hmmsearch_output )
  43       Util.check_file_for_readability( fasta_sequence_file )
  44       Util.check_file_for_writability( outfile )
  45       Util.check_file_for_writability( passed_seqs_outfile )
  46       Util.check_file_for_writability( failed_seqs_outfile )
  47
  48       in_msa = nil
  49       factory = MsaFactory.new()
  50       in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
  51
  52       if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
  53         error_msg = "could not find fasta sequences in " + fasta_sequence_file
  54         raise IOError, error_msg
  55       end
  56
  57       out_msa = Msa.new
  58       failed_seqs = Msa.new
  59       passed_seqs = Msa.new
  60
  61       ld = Constants::LINE_DELIMITER
  62
  63       domain_pass_counter     = 0
  64       domain_fail_counter     = 0
  65       proteins_with_passing_domains = 0
  66       proteins_with_failing_domains = 0
  67       max_domain_copy_number_per_protein = -1
  68       max_domain_copy_number_sequence    = ''
  69       failed_species_counts         = Hash.new
  70       passed_species_counts         = Hash.new
  71
  72       File.open( hmmsearch_output ) do | file |
  73         while line = file.gets
  74           if !is_ignorable?( line ) && line =~ /^\S+\s+/
  75
  76             #         tn      acc     tlen    query   acc     qlen    Evalue  score   bias    #       of      c-E     i-E     score   bias    hf      ht      af      at      ef      et      acc     desc
  77             #         1       2       3       4       5       6       7       8       9       10      11      12      13      14      15      16      17      18      19      20      21      22      23
  78             line =~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/
  79
  80             target_name = $1
  81             if domain_id != target_name
  82               next
  83             end
  84
  85
  86             sequence = $4
  87             number   = $10.to_i
  88             out_of   = $11.to_i
  89             env_from = $20.to_i
  90             env_to   = $21.to_i
  91             i_e_value  = $13.to_f
  92             if ( number > max_domain_copy_number_per_protein )
  93               max_domain_copy_number_sequence    = sequence
  94               max_domain_copy_number_per_protein = number
  95             end
  96             if ( ( ( e_value_threshold.to_f < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
  97                  ( ( length_threshold.to_f <= 0 )   || ( env_to - env_from + 1 ) >= length_threshold.to_f )  )
  98               extract_domain( sequence,
  99                 number,
 100                 out_of,
 101                 env_from,
 102                 env_to,
 103                 in_msa,
 104                 out_msa,
 105                 add_position,
 106                 add_domain_number,
 107                 add_domain_number_as_digit,
 108                 add_domain_number_as_letter,
 109                 trim_name )
 110               domain_pass_counter += 1
 111               count_species( sequence, passed_species_counts )
 112               if passed_seqs.find_by_name_start( sequence, true ).length < 1
 113                 add_sequence( sequence, in_msa, passed_seqs )
 114                 proteins_with_passing_domains += 1
 115               end
 116             else
 117               print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
 118               log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
 119               if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
 120                 print( " iE=" + i_e_value.to_s )
 121                 log << " iE=" + i_e_value.to_s
 122               end
 123               if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
 124                 le = env_to - env_from + 1
 125                 print( " l=" + le.to_s )
 126                 log << " l=" + le.to_s
 127               end
 128               print( Constants::LINE_DELIMITER )
 129               log << Constants::LINE_DELIMITER
 130               domain_fail_counter  += 1
 131               count_species( sequence, failed_species_counts )
 132               if failed_seqs.find_by_name_start( sequence, true ).length < 1
 133                 add_sequence( sequence, in_msa, failed_seqs )
 134                 proteins_with_failing_domains += 1
 135               end
 136             end
 137           end
 138         end
 139       end
 140
 141       if domain_pass_counter < 1
 142         error_msg = "no domain sequences were extracted"
 143         raise StandardError, error_msg
 144       end
 145
 146       log << Constants::LINE_DELIMITER
 147       puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
 148       log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
 149       log << Constants::LINE_DELIMITER
 150
 151       if ( max_domain_copy_number_per_protein > 1 )
 152         puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
 153         log << "First protein with this copy number: " + max_domain_copy_number_sequence
 154         log << Constants::LINE_DELIMITER
 155       end
 156
 157       io = MsaIO.new()
 158       w = FastaWriter.new()
 159       w.set_line_width( 60 )
 160       w.clean( true )
 161
 162       begin
 163         io.write_to_file( out_msa, outfile, w )
 164       rescue Exception
 165         error_msg = "could not write to \"" + outfile + "\""
 166         raise IOError, error_msg
 167       end
 168
 169       begin
 170         io.write_to_file( passed_seqs, passed_seqs_outfile, w )
 171       rescue Exception
 172         error_msg = "could not write to \"" + passed_seqs_outfile + "\""
 173         raise IOError, error_msg
 174       end
 175
 176       begin
 177         io.write_to_file( failed_seqs, failed_seqs_outfile, w )
 178       rescue Exception
 179         error_msg = "could not write to \"" + failed_seqs_outfile + "\""
 180         raise IOError, error_msg
 181       end
 182
 183       log << ld
 184       log << "passing domains              : " + domain_pass_counter.to_s + ld
 185       log << "failing domains              : " + domain_fail_counter.to_s + ld
 186       log << "proteins with passing domains: " + proteins_with_passing_domains.to_s + ld
 187       log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
 188       log << ld
 189       log << 'passing domains counts per species: ' << ld
 190       passed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld }
 191       log << ld
 192       log << 'failing domains counts per species: ' << ld
 193       failed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld }
 194       log << ld
 195       return domain_pass_counter
 196
 197     end # parse
 198
 199     private
 200
 201
 202     def add_sequence( sequence_name, in_msa, add_to_msa )
 203       seqs = in_msa.find_by_name_start( sequence_name, true )
 204       if ( seqs.length < 1 )
 205         error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
 206         raise StandardError, error_msg
 207       end
 208       if ( seqs.length > 1 )
 209         error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
 210         raise StandardError, error_msg
 211       end
 212       seq = in_msa.get_sequence( seqs[ 0 ] )
 213       add_to_msa.add_sequence( seq )
 214     end
 215
 216     # raises ArgumentError, StandardError
 217     def extract_domain( sequence,
 218         number,
 219         out_of,
 220         seq_from,
 221         seq_to,
 222         in_msa,
 223         out_msa,
 224         add_position,
 225         add_domain_number,
 226         add_domain_number_as_digit,
 227         add_domain_number_as_letter,
 228         trim_name )
 229       if ( number < 1 || out_of < 1 || number > out_of )
 230         error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
 231         raise ArgumentError, error_msg
 232       end
 233       if ( seq_from < 1 || seq_to < 1 || seq_from >= seq_to )
 234         error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
 235         raise ArgumentError, error_msg
 236       end
 237       seqs = in_msa.find_by_name_start( sequence, true )
 238       if seqs.length < 1
 239         error_msg = "sequence \"" + sequence + "\" not found in sequence file"
 240         raise StandardError, error_msg
 241       end
 242       if seqs.length > 1
 243         error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
 244         raise StandardError, error_msg
 245       end
 246       # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
 247       seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
 248
 249       seq.set_name( seq.get_name.split[ 0 ] )
 250
 251       if add_position
 252         seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
 253       end
 254
 255       if trim_name
 256         seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] )
 257       end
 258
 259       if out_of != 1
 260         if ( add_domain_number_as_digit )
 261           seq.set_name( seq.get_name + number.to_s )
 262         elsif ( add_domain_number_as_letter )
 263           if number > 25
 264             error_msg = 'too many identical domains per sequence, cannot use letters to distinguish them'
 265             raise StandardError, error_msg
 266           end
 267           seq.set_name( seq.get_name + ( number + 96 ).chr )
 268         elsif ( add_domain_number )
 269           seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
 270         end
 271       end
 272
 273       # if ( seq.get_name.length > 10 )
 274       #   error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters"
 275       #   raise StandardError, error_msg
 276       # end
 277
 278       out_msa.add_sequence( seq )
 279     end
 280
 281     def count_species( sequence, species_counts_map )
 282       species = get_species( sequence )
 283       if species != nil
 284         if !species_counts_map.has_key?( species )
 285           species_counts_map[ species ] = 1
 286         else
 287           species_counts_map[ species ] = species_counts_map[ species ] + 1
 288         end
 289       end
 290     end
 291
 292     def get_species( sequence_name )
 293       if sequence_name =~ /^.+_(.+)$/
 294         return $1
 295       else
 296         return nil
 297       end
 298     end
 299
 300     def is_ignorable?( line )
 301       return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
 302     end
 303
 304   end # class HmmscanDomainExtractor
 305
 306 end # module Evoruby
 307