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 # last modified: 121003
  10
  11 require 'set'
  12
  13 require 'lib/evo/util/constants'
  14 require 'lib/evo/util/util'
  15 require 'lib/evo/util/command_line_arguments'
  16 require 'lib/evo/io/parser/hmmscan_parser'
  17 require 'lib/evo/io/web/uniprotkb'
  18
  19 module Evoruby
  20
  21   class HmmscanSummary
  22
  23     PRG_NAME       = "hsp"
  24     PRG_VERSION    = "2.000"
  25     PRG_DESC       = "hmmscan summary"
  26     PRG_DATE       = "2012.10.23"
  27     COPYRIGHT      = "2012 Christian M Zmasek"
  28     CONTACT        = "phylosoft@gmail.com"
  29     WWW            = "www.phylosoft.org"
  30
  31     DELIMITER_OPTION              = "d"
  32     SPECIES_OPTION                = "s"
  33     I_E_VALUE_THRESHOLD_OPTION    = "ie"
  34     FS_E_VALUE_THRESHOLD_OPTION   = "pe"
  35     HMM_FOR_PROTEIN_OUTPUT        = "m"
  36     IGNORE_DUF_OPTION             = "i"
  37     PARSE_OUT_DESCRIPITION_OPTION = "a"
  38     UNIPROT                       = "u"
  39     HELP_OPTION_1                 = "help"
  40     HELP_OPTION_2                 = "h"
  41
  42     USE_AVOID_HMMS = true
  43     AVOID_HHMS = [ "RRM_1", "RRM_2", "RRM_3", "RRM_4", "RRM_5", "RRM_6" ]
  44     LIMIT_FOR_CLOSE_DOMAINS = 20
  45
  46     def initialize
  47       @domain_counts = Hash.new
  48     end
  49
  50     def run
  51
  52
  53
  54       Util.print_program_information( PRG_NAME,
  55         PRG_VERSION,
  56         PRG_DESC,
  57         PRG_DATE,
  58         COPYRIGHT,
  59         CONTACT,
  60         WWW,
  61         STDOUT )
  62
  63       begin
  64         cla = CommandLineArguments.new( ARGV )
  65       rescue ArgumentError => e
  66         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
  67       end
  68
  69       if ( cla.is_option_set?( HELP_OPTION_1 ) ||
  70             cla.is_option_set?( HELP_OPTION_2 ) )
  71         print_help
  72         exit( 0 )
  73       end
  74
  75       if ( cla.get_number_of_files != 2 )
  76         print_help
  77         exit( -1 )
  78       end
  79
  80       allowed_opts = Array.new
  81       allowed_opts.push( DELIMITER_OPTION )
  82       allowed_opts.push( I_E_VALUE_THRESHOLD_OPTION )
  83       allowed_opts.push( FS_E_VALUE_THRESHOLD_OPTION )
  84       allowed_opts.push( IGNORE_DUF_OPTION )
  85       allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
  86       allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT )
  87       allowed_opts.push( UNIPROT )
  88       allowed_opts.push( SPECIES_OPTION )
  89
  90       disallowed = cla.validate_allowed_options_as_str( allowed_opts )
  91       if ( disallowed.length > 0 )
  92         Util.fatal_error( PRG_NAME,
  93           "unknown option(s): " + disallowed,
  94           STDOUT )
  95       end
  96
  97       inpath = cla.get_file_name( 0 )
  98       outpath = cla.get_file_name( 1 )
  99
 100       column_delimiter = "\t"
 101       if ( cla.is_option_set?( DELIMITER_OPTION ) )
 102         begin
 103           column_delimiter = cla.get_option_value( DELIMITER_OPTION )
 104         rescue ArgumentError => e
 105           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 106         end
 107       end
 108
 109       i_e_value_threshold = -1.0
 110       if ( cla.is_option_set?( I_E_VALUE_THRESHOLD_OPTION ) )
 111         begin
 112           i_e_value_threshold = cla.get_option_value_as_float( I_E_VALUE_THRESHOLD_OPTION )
 113         rescue ArgumentError => e
 114           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 115         end
 116         if ( i_e_value_threshold < 0.0 )
 117           Util.fatal_error( PRG_NAME, "attempt to use a negative i-E-value threshold", STDOUT )
 118         end
 119       end
 120
 121
 122
 123       fs_e_value_threshold = -1.0
 124       if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
 125         begin
 126           fs_e_value_threshold = cla.get_option_value_as_float( FS_E_VALUE_THRESHOLD_OPTION )
 127         rescue ArgumentError => e
 128           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 129         end
 130         if ( fs_e_value_threshold < 0.0 )
 131           Util.fatal_error( PRG_NAME, "attempt to use a negative E-value threshold", STDOUT )
 132         end
 133       end
 134
 135       hmm_for_protein_output = ""
 136       if ( cla.is_option_set?( HMM_FOR_PROTEIN_OUTPUT ) )
 137         begin
 138           hmm_for_protein_output = cla.get_option_value( HMM_FOR_PROTEIN_OUTPUT )
 139         rescue ArgumentError => e
 140           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 141         end
 142       end
 143
 144       uniprot = ""
 145       if ( cla.is_option_set?( UNIPROT ) )
 146         begin
 147           uniprot = cla.get_option_value( UNIPROT )
 148         rescue ArgumentError => e
 149           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 150         end
 151       end
 152
 153       species = "HUMAN"
 154        if ( cla.is_option_set?( SPECIES_OPTION ) )
 155         begin
 156           species = cla.get_option_value( SPECIES_OPTION )
 157         rescue ArgumentError => e
 158           Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 159         end
 160       end
 161
 162       ignore_dufs = false
 163       if ( cla.is_option_set?( IGNORE_DUF_OPTION ) )
 164         ignore_dufs = true
 165       end
 166
 167       parse_descriptions = false
 168       if ( cla.is_option_set?( PARSE_OUT_DESCRIPITION_OPTION ) )
 169         parse_descriptions = true
 170       end
 171
 172       puts()
 173       puts( "hmmpfam outputfile  : " + inpath )
 174       puts( "outputfile          : " + outpath )
 175       puts( "species             : " + species )
 176       if ( i_e_value_threshold >= 0.0 )
 177         puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
 178       else
 179         puts( "i-E-value threshold : no threshold" )
 180       end
 181       if ( parse_descriptions )
 182         puts( "parse descriptions  : true" )
 183       else
 184         puts( "parse descriptions  : false" )
 185       end
 186       if ( ignore_dufs )
 187         puts( "ignore DUFs         : true" )
 188       else
 189         puts( "ignore DUFs         : false" )
 190       end
 191       if ( column_delimiter == "\t" )
 192         puts( "column delimiter    : TAB" )
 193       else
 194         puts( "column delimiter     : " + column_delimiter )
 195       end
 196       if fs_e_value_threshold >= 0.0
 197         puts( "E-value threshold   : " + fs_e_value_threshold.to_s )
 198       else
 199         puts( "E-value threshold   : no threshold" )
 200       end
 201       if !hmm_for_protein_output.empty?
 202         puts( "HMM for proteins    : " + hmm_for_protein_output )
 203       end
 204       if !uniprot.empty?
 205         puts( "Uniprot             : " + uniprot )
 206       end
 207       puts()
 208
 209       begin
 210         parse( inpath,
 211           outpath,
 212           column_delimiter,
 213           i_e_value_threshold,
 214           ignore_dufs,
 215           parse_descriptions,
 216           fs_e_value_threshold,
 217           hmm_for_protein_output,
 218           uniprot,
 219           species )
 220       rescue IOError => e
 221         Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
 222       end
 223       domain_counts = get_domain_counts()
 224
 225
 226       puts
 227       puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
 228       puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
 229       puts
 230       puts( Util.draw_histogram( domain_counts, "#" ) )
 231       puts
 232       Util.print_message( PRG_NAME, 'OK' )
 233       puts
 234
 235     end # def run
 236
 237     private
 238
 239     # raises ArgumentError, IOError
 240     def parse( inpath,
 241         outpath,
 242         column_delimiter,
 243         i_e_value_threshold,
 244         ignore_dufs,
 245         get_descriptions,
 246         fs_e_value_threshold,
 247         hmm_for_protein_output,
 248         uniprot,
 249         species )
 250
 251
 252
 253       Util.check_file_for_readability( inpath )
 254       Util.check_file_for_writability( outpath )
 255
 256       hmmscan_parser = HmmscanParser.new( inpath )
 257       results = hmmscan_parser.parse
 258
 259       outfile = File.open( outpath, "a" )
 260
 261       query     = ""
 262       desc      = ""
 263       model     = ""
 264       env_from  = ""
 265       env_to    = ""
 266       i_e_value = ""
 267
 268       hmmscan_results_per_protein = []
 269
 270
 271
 272       prev_query = ""
 273
 274       results.each do | r |
 275         model     = r.model
 276         query     = r.query
 277         i_e_value = r.i_e_value
 278         env_from  = r.env_from
 279         env_to    = r.env_to
 280
 281         if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) &&
 282             ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
 283           count_model( model )
 284           outfile.print( query +
 285               column_delimiter )
 286           if ( get_descriptions )
 287             outfile.print( desc +
 288                 column_delimiter )
 289           end
 290           outfile.print( model +
 291               column_delimiter +
 292               env_from.to_s +
 293               column_delimiter +
 294               env_to.to_s +
 295               column_delimiter +
 296               i_e_value.to_s )
 297           outfile.print( Constants::LINE_DELIMITER )
 298         end
 299
 300         if !hmm_for_protein_output.empty?
 301           if  !prev_query.empty? && prev_query != query
 302             if !hmmscan_results_per_protein.empty?
 303               process_hmmscan_results_per_protein( hmmscan_results_per_protein,
 304                 fs_e_value_threshold,
 305                 hmm_for_protein_output,
 306                 i_e_value_threshold,
 307                 true )
 308             end
 309             hmmscan_results_per_protein.clear
 310           end
 311           prev_query = query
 312
 313           if USE_AVOID_HMMS
 314             if !AVOID_HHMS.include? r.model
 315               hmmscan_results_per_protein << r
 316             end
 317           else
 318             hmmscan_results_per_protein << r
 319           end
 320         end
 321       end
 322       if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
 323         process_hmmscan_results_per_protein( hmmscan_results_per_protein,
 324           fs_e_value_threshold,
 325           hmm_for_protein_output,
 326           i_e_value_threshold,
 327           true )
 328       end
 329
 330       outfile.flush()
 331       outfile.close()
 332
 333     end # def parse
 334
 335     def process_id( id )
 336       if  id =~ /(sp|tr)\|\S+\|(\S+)/
 337         id = $2
 338       end
 339       id
 340     end
 341
 342
 343
 344     def count_model( model )
 345       if ( @domain_counts.has_key?( model ) )
 346         count = @domain_counts[ model ].to_i
 347         count += 1
 348         @domain_counts[ model ] = count
 349       else
 350         @domain_counts[ model ] = 1
 351       end
 352     end
 353
 354     def process_hmmscan_results_per_protein( hmmscan_results_per_protein,
 355         fs_e_value_threshold,
 356         hmm_for_protein_output,
 357         i_e_value_threshold,
 358         uniprotkb )
 359
 360       dc = 0
 361       # filter according to i-Evalue threshold
 362       # abort if fs Evalue too high
 363       hmmscan_results_per_protein_filtered = []
 364
 365       hmmscan_results_per_protein.each do | r |
 366         if r.model == hmm_for_protein_output
 367           if r.fs_e_value > fs_e_value_threshold
 368             return
 369           end
 370         end
 371         if r.i_e_value <= i_e_value_threshold
 372           hmmscan_results_per_protein_filtered << r
 373           if r.model == hmm_for_protein_output
 374             dc += 1
 375           end
 376         end
 377       end
 378
 379       if dc == 0
 380         # passed on protein E-value, failed in per domain E-values
 381         return
 382       end
 383
 384       hmmscan_results_per_protein_filtered.sort! { |r1,r2| r1.env_from <=> r2.env_from }
 385
 386       own = nil
 387       hmmscan_results_per_protein_filtered.each do | r |
 388         if r.model == hmm_for_protein_output
 389           own = r
 390         end
 391       end
 392
 393       s = ""
 394       s << own.query + "\t"
 395       s << species + "\t"
 396       s << own.fs_e_value.to_s + "\t"
 397       s << own.qlen.to_s + "\t"
 398       s << dc.to_s + "\t"
 399       s << hmmscan_results_per_protein_filtered.length.to_s + "\t"
 400       hmmscan_results_per_protein_filtered.each do | r |
 401         s << r.model + " "
 402       end
 403       s << "\t"
 404       e = UniprotKB::get_entry_by_id( process_id( own.query ) )
 405
 406       if e != nil
 407         s << uniprot_annotation( e )
 408        # s << "\uniprot_annotationt"
 409       end
 410
 411       overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 412
 413       s << overview  + "\t"
 414
 415       s << calc_linkers(  hmmscan_results_per_protein_filtered, hmm_for_protein_output )  + "\t"
 416
 417       prev_r = nil
 418       hmmscan_results_per_protein_filtered.each do | r |
 419
 420         if  prev_r != nil
 421           s << make_interdomain_sequence( r.env_from - prev_r.env_to - 1 )
 422         else
 423           s << make_interdomain_sequence( r.env_from, false )
 424         end
 425         s << r.model
 426         s << "["
 427         s << r.env_from.to_s << "-" << r.env_to.to_s
 428         s << "|ie=" << r.i_e_value.to_s
 429         s << "|ce=" << r.c_e_value.to_s
 430         s << "]"
 431         prev_r = r
 432       end
 433       s << make_interdomain_sequence( own.qlen - prev_r.env_from, false )
 434       puts s
 435     end
 436
 437     def uniprot_annotation( e )
 438       s = ""
 439       pdb_ids = e.get_pdb_ids
 440       if !pdb_ids.empty?
 441         pdb_ids.each do | pdb |
 442           s << pdb << ", "
 443         end
 444       else
 445         s << "-"
 446       end
 447       s
 448     end
 449
 450     def calc_linkers(  hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 451       linkers = ""
 452       prev_r = nil
 453       hmmscan_results_per_protein_filtered.each do | r |
 454         if r.model == hmm_for_protein_output
 455           if  prev_r != nil
 456             linkers << ( r.env_from - prev_r.env_to - 1 ).to_s + " "
 457           end
 458           prev_r = r
 459         end
 460       end
 461       linkers
 462     end
 463
 464     def get_domain_counts()
 465       return @domain_counts
 466     end
 467
 468     def make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
 469       overview = ""
 470       prev_r = nil
 471       hmmscan_results_per_protein_filtered.each do | r |
 472         if r.model == hmm_for_protein_output
 473           if prev_r == nil
 474             overview << hmm_for_protein_output
 475           else
 476             if  ( r.env_from - prev_r.env_to - 1 ) <= LIMIT_FOR_CLOSE_DOMAINS
 477               overview << "~" << hmm_for_protein_output
 478             else
 479               overview << "----" << hmm_for_protein_output
 480             end
 481           end
 482           prev_r = r
 483         end
 484       end
 485       overview
 486     end
 487
 488     def make_interdomain_sequence( d, mark_short = true )
 489       s = ""
 490       d /= 20
 491       if d >= 10
 492         s << "----//----"
 493       elsif d >= 1
 494         d.times do
 495           s << "-"
 496         end
 497       elsif mark_short
 498         s << "~"
 499       end
 500       s
 501     end
 502
 503
 504
 505     def print_help()
 506       puts( "Usage:" )
 507       puts()
 508       puts( "  " + PRG_NAME + ".rb [options] <hmmscan outputfile> <outputfile>" )
 509       puts()
 510       puts( "  options: -" + DELIMITER_OPTION + ": column delimiter for outputfile, default is TAB" )
 511       puts( "           -" + I_E_VALUE_THRESHOLD_OPTION  + ": i-E-value threshold, default is no threshold" )
 512       puts( "           -" + PARSE_OUT_DESCRIPITION_OPTION  + ": parse query description (in addition to query name)" )
 513       puts( "           -" + IGNORE_DUF_OPTION  + ": ignore DUFs" )
 514       puts( "           -" + FS_E_VALUE_THRESHOLD_OPTION  + ": E-value threshold for full protein sequences, only for protein summary" )
 515       puts( "           -" + HMM_FOR_PROTEIN_OUTPUT + ": HMM for protein summary" )
 516       puts()
 517     end
 518
 519   end # class
 520
 521 end # module Evoruby