forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb

   1 #
   2 # = lib/evo/tool/hmmscan_summary.rb - HmmscanSummary class
   3 #
   4 # Copyright::  Copyright (C) 2012 Christian M. Zmasek
   5 # License::    GNU Lesser General Public License (LGPL)
   6 #
   7 # $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $
   8 #
   9
  10 require 'set'
  11
  12 require 'lib/evo/util/constants'
  13 require 'lib/evo/util/util'
  14 require 'lib/evo/util/command_line_arguments'
  15 require 'lib/evo/io/parser/hmmscan_parser'
  16
  17 module Evoruby
  18
  19   class HmmscanSummary
  20
  21     PRG_NAME       = "hsp"
  22     PRG_VERSION    = "2.002"
  23     PRG_DESC       = "hmmscan summary"
  24     PRG_DATE       = "130319"
  25     COPYRIGHT      = "2013 Christian M Zmasek"
  26     CONTACT        = "phyloxml@gmail.com"
  27     WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"
  28
  29     DELIMITER_OPTION              = "d"
  30     SPECIES_OPTION                = "s"
  31     I_E_VALUE_THRESHOLD_OPTION    = "ie"
  32     FS_E_VALUE_THRESHOLD_OPTION   = "pe"
  33     HMM_FOR_PROTEIN_OUTPUT        = "m"
  34     IGNORE_DUF_OPTION             = "i"
  35     PARSE_OUT_DESCRIPITION_OPTION = "a"
  36     HELP_OPTION_1                 = "help"
  37     HELP_OPTION_2                 = "h"
  38
  39     USE_AVOID_HMMS = true
  40     AVOID_HHMS = [ "RRM_1", "RRM_2", "RRM_3", "RRM_4", "RRM_5", "RRM_6" ]
  41     LIMIT_FOR_CLOSE_DOMAINS = 20
  42
  43     def initialize
  44       @domain_counts = Hash.new
  45     end
  46
  47     def run
  48
  49       Util.print_program_information( PRG_NAME,
  50         PRG_VERSION,
  51         PRG_DESC,
  52         PRG_DATE,
  53         COPYRIGHT,
  54         CONTACT,
  55         WWW,
  56         STDOUT )
  57
  58       begin
  59         cla = CommandLineArguments.new( ARGV )
  60       rescue ArgumentError => e
  61         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
  62       end
  63
  64       if ( cla.is_option_set?( HELP_OPTION_1 ) ||
  65            cla.is_option_set?( HELP_OPTION_2 ) )
  66         print_help
  67         exit( 0 )
  68       end
  69
  70       if ( cla.get_number_of_files != 2 )
  71         print_help
  72         exit( -1 )
  73       end
  74
  75       allowed_opts = Array.new
  76       allowed_opts.push( DELIMITER_OPTION )
  77       allowed_opts.push( I_E_VALUE_THRESHOLD_OPTION )
  78       allowed_opts.push( FS_E_VALUE_THRESHOLD_OPTION )
  79       allowed_opts.push( IGNORE_DUF_OPTION )
  80       allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
  81       allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT )
  82       allowed_opts.push( SPECIES_OPTION )
  83
  84       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
  85       if ( disallowed.length > 0 )
  86         Util.fatal_error( PRG_NAME,
  87           "unknown option(s): " + disallowed,
  88           STDOUT )
  89       end
  90
  91       inpath = cla.get_file_name( 0 )
  92       outpath = cla.get_file_name( 1 )
  93
  94       column_delimiter = "\t"
  95       if ( cla.is_option_set?( DELIMITER_OPTION ) )
  96         begin
  97           column_delimiter = cla.get_option_value( DELIMITER_OPTION )
  98         rescue ArgumentError => e
  99           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 100         end
 101       end
 102
 103       i_e_value_threshold = -1.0
 104       if ( cla.is_option_set?( I_E_VALUE_THRESHOLD_OPTION ) )
 105         begin
 106           i_e_value_threshold = cla.get_option_value_as_float( I_E_VALUE_THRESHOLD_OPTION )
 107         rescue ArgumentError => e
 108           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 109         end
 110         if ( i_e_value_threshold < 0.0 )
 111           Util.fatal_error( PRG_NAME, "attempt to use a negative i-E-value threshold", STDOUT )
 112         end
 113       end
 114
 115       fs_e_value_threshold = -1.0
 116       if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
 117         begin
 118           fs_e_value_threshold = cla.get_option_value_as_float( FS_E_VALUE_THRESHOLD_OPTION )
 119         rescue ArgumentError => e
 120           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 121         end
 122         if ( fs_e_value_threshold < 0.0 )
 123           Util.fatal_error( PRG_NAME, "attempt to use a negative E-value threshold", STDOUT )
 124         end
 125       end
 126
 127       hmm_for_protein_output = ""
 128       if ( cla.is_option_set?( HMM_FOR_PROTEIN_OUTPUT ) )
 129         begin
 130           hmm_for_protein_output = cla.get_option_value( HMM_FOR_PROTEIN_OUTPUT )
 131         rescue ArgumentError => e
 132           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 133         end
 134       end
 135
 136       species = "HUMAN"
 137       if ( cla.is_option_set?( SPECIES_OPTION ) )
 138         begin
 139           species = cla.get_option_value( SPECIES_OPTION )
 140         rescue ArgumentError => e
 141           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 142         end
 143       end
 144
 145       ignore_dufs = false
 146       if ( cla.is_option_set?( IGNORE_DUF_OPTION ) )
 147         ignore_dufs = true
 148       end
 149
 150       parse_descriptions = false
 151       if ( cla.is_option_set?( PARSE_OUT_DESCRIPITION_OPTION ) )
 152         parse_descriptions = true
 153       end
 154
 155       puts()
 156       puts( "hmmpfam outputfile  : " + inpath )
 157       puts( "outputfile          : " + outpath )
 158       puts( "species             : " + species )
 159       if ( i_e_value_threshold >= 0.0 )
 160         puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
 161       else
 162         puts( "i-E-value threshold : no threshold" )
 163       end
 164       if ( parse_descriptions )
 165         puts( "parse descriptions  : true" )
 166       else
 167         puts( "parse descriptions  : false" )
 168       end
 169       if ( ignore_dufs )
 170         puts( "ignore DUFs         : true" )
 171       else
 172         puts( "ignore DUFs         : false" )
 173       end
 174       if ( column_delimiter == "\t" )
 175         puts( "column delimiter    : TAB" )
 176       else
 177         puts( "column delimiter     : " + column_delimiter )
 178       end
 179       if fs_e_value_threshold >= 0.0
 180         puts( "E-value threshold   : " + fs_e_value_threshold.to_s )
 181       else
 182         puts( "E-value threshold   : no threshold" )
 183       end
 184       if !hmm_for_protein_output.empty?
 185         puts( "HMM for proteins    : " + hmm_for_protein_output )
 186       end
 187       puts()
 188
 189       begin
 190         parse( inpath,
 191           outpath,
 192           column_delimiter,
 193           i_e_value_threshold,
 194           ignore_dufs,
 195           parse_descriptions,
 196           fs_e_value_threshold,
 197           hmm_for_protein_output,
 198           species )
 199       rescue IOError => e
 200         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 201       end
 202       domain_counts = get_domain_counts()
 203
 204       puts
 205       puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
 206       puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
 207       puts
 208       puts( Util.draw_histogram( domain_counts, "#" ) )
 209       puts
 210       Util.print_message( PRG_NAME, 'OK' )
 211       puts
 212
 213     end # def run
 214
 215     private
 216
 217     # raises ArgumentError, IOError
 218     def parse( inpath,
 219         outpath,
 220         column_delimiter,
 221         i_e_value_threshold,
 222         ignore_dufs,
 223         get_descriptions,
 224         fs_e_value_threshold,
 225         hmm_for_protein_output,
 226         species )
 227
 228       Util.check_file_for_readability( inpath )
 229       Util.check_file_for_writability( outpath )
 230
 231       hmmscan_parser = HmmscanParser.new( inpath )
 232       results = hmmscan_parser.parse
 233
 234       outfile = File.open( outpath, "a" )
 235
 236       query     = ""
 237       desc      = ""
 238       model     = ""
 239       env_from  = ""
 240       env_to    = ""
 241       i_e_value = ""
 242
 243       hmmscan_results_per_protein = []
 244
 245       prev_query = ""
 246
 247       results.each do | r |
 248         model     = r.model
 249         query     = r.query
 250         i_e_value = r.i_e_value
 251         env_from  = r.env_from
 252         env_to    = r.env_to
 253
 254         if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) &&
 255            ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
 256           count_model( model )
 257           outfile.print( query +
 258              column_delimiter )
 259           if ( get_descriptions )
 260             outfile.print( desc +
 261                column_delimiter )
 262           end
 263           outfile.print( model +
 264              column_delimiter +
 265              env_from.to_s +
 266              column_delimiter +
 267              env_to.to_s +
 268              column_delimiter +
 269              i_e_value.to_s )
 270           outfile.print( Constants::LINE_DELIMITER )
 271         end
 272
 273         if !hmm_for_protein_output.empty?
 274           if  !prev_query.empty? && prev_query != query
 275             if !hmmscan_results_per_protein.empty?
 276               process_hmmscan_results_per_protein( hmmscan_results_per_protein,
 277                 fs_e_value_threshold,
 278                 hmm_for_protein_output,
 279                 i_e_value_threshold,
 280                 species )
 281             end
 282             hmmscan_results_per_protein.clear
 283           end
 284           prev_query = query
 285
 286           if USE_AVOID_HMMS
 287             if !AVOID_HHMS.include? r.model
 288               hmmscan_results_per_protein << r
 289             end
 290           else
 291             hmmscan_results_per_protein << r
 292           end
 293         end
 294       end
 295
 296       if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
 297         process_hmmscan_results_per_protein( hmmscan_results_per_protein,
 298           fs_e_value_threshold,
 299           hmm_for_protein_output,
 300           i_e_value_threshold,
 301           species )
 302       end
 303
 304       outfile.flush()
 305       outfile.close()
 306     end # def parse
 307
 308     def process_id( id )
 309       if  id =~ /(sp|tr)\|\S+\|(\S+)/
 310         id = $2
 311       end
 312       id
 313     end
 314
 315     def count_model( model )
 316       if ( @domain_counts.has_key?( model ) )
 317         count = @domain_counts[ model ].to_i
 318         count += 1
 319         @domain_counts[ model ] = count
 320       else
 321         @domain_counts[ model ] = 1
 322       end
 323     end
 324
 325     def process_hmmscan_results_per_protein( hmmscan_results_per_protein,
 326         fs_e_value_threshold,
 327         hmm_for_protein_output,
 328         i_e_value_threshold,
 329         species )
 330
 331       dc = 0
 332       # filter according to i-Evalue threshold
 333       # abort if fs Evalue too high
 334       hmmscan_results_per_protein_filtered = []
 335
 336       hmmscan_results_per_protein.each do | r |
 337
 338
 339         if r.model == hmm_for_protein_output
 340           if fs_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold
 341             return
 342           end
 343         end
 344         if i_e_value_threshold <= 0 || r.i_e_value <= i_e_value_threshold
 345           hmmscan_results_per_protein_filtered << r
 346           if r.model == hmm_for_protein_output
 347             dc += 1
 348           end
 349         end
 350       end
 351
 352       if dc == 0
 353         # passed on protein E-value, failed in per domain E-values
 354         return
 355       end
 356
 357       hmmscan_results_per_protein_filtered.sort! { |r1,r2| r1.env_from <=> r2.env_from }
 358
 359       own = nil
 360       hmmscan_results_per_protein_filtered.each do | r |
 361         if r.model == hmm_for_protein_output
 362           own = r
 363         end
 364       end
 365
 366       s = ""
 367       s << own.query + "\t"
 368       s << species + "\t"
 369       s << own.fs_e_value.to_s + "\t"
 370       s << own.qlen.to_s + "\t"
 371       s << dc.to_s + "\t"
 372       s << hmmscan_results_per_protein_filtered.length.to_s + "\t"
 373       hmmscan_results_per_protein_filtered.each do | r |
 374         s << r.model + " "
 375       end
 376       s << "\t"
 377
 378       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 379
 380       s << overview  + "\t"
 381
 382       s << calc_linkers(  hmmscan_results_per_protein_filtered, hmm_for_protein_output )  + "\t"
 383
 384       prev_r = nil
 385       hmmscan_results_per_protein_filtered.each do | r |
 386         if  prev_r != nil
 387           s << make_interdomain_sequence( r.env_from - prev_r.env_to - 1 )
 388         else
 389           s << make_interdomain_sequence( r.env_from, false )
 390         end
 391         s << r.model
 392         s << "["
 393         s << r.env_from.to_s << "-" << r.env_to.to_s
 394         s << "|ie=" << r.i_e_value.to_s
 395         s << "|ce=" << r.c_e_value.to_s
 396         s << "]"
 397         prev_r = r
 398       end
 399       s << make_interdomain_sequence( own.qlen - prev_r.env_to, false )
 400       puts s
 401     end
 402
 403     def calc_linkers(  hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 404       linkers = ""
 405       prev_r = nil
 406       hmmscan_results_per_protein_filtered.each do | r |
 407         if r.model == hmm_for_protein_output
 408           if  prev_r != nil
 409             linkers << ( r.env_from - prev_r.env_to - 1 ).to_s + " "
 410           end
 411           prev_r = r
 412         end
 413       end
 414       linkers
 415     end
 416
 417     def get_domain_counts()
 418       return @domain_counts
 419     end
 420
 421     def make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 422       overview = ""
 423       prev_r = nil
 424       hmmscan_results_per_protein_filtered.each do | r |
 425         if r.model == hmm_for_protein_output
 426           if prev_r == nil
 427             overview << hmm_for_protein_output
 428           else
 429             if  ( r.env_from - prev_r.env_to - 1 ) <= LIMIT_FOR_CLOSE_DOMAINS
 430               overview << "~" << hmm_for_protein_output
 431             else
 432               overview << "----" << hmm_for_protein_output
 433             end
 434           end
 435           prev_r = r
 436         end
 437       end
 438       overview
 439     end
 440
 441     def make_interdomain_sequence( d, mark_short = true )
 442       s = ""
 443       d /= 20
 444       if d >= 10
 445         s << "----//----"
 446       elsif d >= 1
 447         d.times do
 448           s << "-"
 449         end
 450       elsif mark_short
 451         s << "~"
 452       end
 453       s
 454     end
 455
 456
 457     def print_help()
 458       puts( "Usage:" )
 459       puts()
 460       puts( "  " + PRG_NAME + ".rb [options] <hmmscan outputfile> <outputfile>" )
 461       puts()
 462       puts( "  options: -" + DELIMITER_OPTION + ": column delimiter for outputfile, default is TAB" )
 463       puts( "           -" + I_E_VALUE_THRESHOLD_OPTION  + ": i-E-value threshold, default is no threshold" )
 464       puts( "           -" + PARSE_OUT_DESCRIPITION_OPTION  + ": parse query description (in addition to query name)" )
 465       puts( "           -" + IGNORE_DUF_OPTION  + ": ignore DUFs" )
 466       puts( "           -" + FS_E_VALUE_THRESHOLD_OPTION  + ": E-value threshold for full protein sequences, only for protein summary" )
 467       puts( "           -" + HMM_FOR_PROTEIN_OUTPUT + ": HMM for protein summary" )
 468       puts( "           -" + SPECIES_OPTION + ": species for protein summary" )
 469       puts()
 470     end
 471
 472   end # class
 473
 474 end # module Evoruby