2 # = lib/evo/tool/hmmscan_summary.rb - HmmscanSummary class
4 # Copyright:: Copyright (C) 2012 Christian M. Zmasek
5 # License:: GNU Lesser General Public License (LGPL)
7 # $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $
9 # last modified: 121003
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/parser/uniprot_parser'
18 require 'lib/evo/io/web/uniprotkb'
26 PRG_DESC = "hmmscan summary"
27 PRG_DATE = "2012.10.23"
28 COPYRIGHT = "2012 Christian M Zmasek"
29 CONTACT = "phylosoft@gmail.com"
30 WWW = "www.phylosoft.org"
32 DELIMITER_OPTION = "d"
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"
39 HELP_OPTION_1 = "help"
43 AVOID_HHMS = [ "RRM_1", "RRM_2", "RRM_3", "RRM_4", "RRM_5", "RRM_6" ]
44 LIMIT_FOR_CLOSE_DOMAINS = 20
47 @domain_counts = Hash.new
55 Util.print_program_information( PRG_NAME,
65 cla = CommandLineArguments.new( ARGV )
66 rescue ArgumentError => e
67 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
70 if ( cla.is_option_set?( HELP_OPTION_1 ) ||
71 cla.is_option_set?( HELP_OPTION_2 ) )
76 if ( cla.get_number_of_files != 2 )
81 allowed_opts = Array.new
82 allowed_opts.push( DELIMITER_OPTION )
83 allowed_opts.push( I_E_VALUE_THRESHOLD_OPTION )
84 allowed_opts.push( FS_E_VALUE_THRESHOLD_OPTION )
85 allowed_opts.push( IGNORE_DUF_OPTION )
86 allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
87 allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT )
88 allowed_opts.push( UNIPROT )
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,
97 inpath = cla.get_file_name( 0 )
98 outpath = cla.get_file_name( 1 )
100 column_delimiter = "\t"
101 if ( cla.is_option_set?( DELIMITER_OPTION ) )
103 column_delimiter = cla.get_option_value( DELIMITER_OPTION )
104 rescue ArgumentError => e
105 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
109 i_e_value_threshold = -1.0
110 if ( cla.is_option_set?( I_E_VALUE_THRESHOLD_OPTION ) )
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 )
116 if ( i_e_value_threshold < 0.0 )
117 Util.fatal_error( PRG_NAME, "attempt to use a negative i-E-value threshold", STDOUT )
121 fs_e_value_threshold = -1.0
122 if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
124 fs_e_value_threshold = cla.get_option_value_as_float( FS_E_VALUE_THRESHOLD_OPTION )
125 rescue ArgumentError => e
126 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
128 if ( fs_e_value_threshold < 0.0 )
129 Util.fatal_error( PRG_NAME, "attempt to use a negative E-value threshold", STDOUT )
133 hmm_for_protein_output = ""
134 if ( cla.is_option_set?( HMM_FOR_PROTEIN_OUTPUT ) )
136 hmm_for_protein_output = cla.get_option_value( HMM_FOR_PROTEIN_OUTPUT )
137 rescue ArgumentError => e
138 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
143 if ( cla.is_option_set?( UNIPROT ) )
145 uniprot = cla.get_option_value( UNIPROT )
146 rescue ArgumentError => e
147 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
152 if ( cla.is_option_set?( IGNORE_DUF_OPTION ) )
156 parse_descriptions = false
157 if ( cla.is_option_set?( PARSE_OUT_DESCRIPITION_OPTION ) )
158 parse_descriptions = true
162 puts( "hmmpfam outputfile : " + inpath )
163 puts( "outputfile : " + outpath )
164 if ( i_e_value_threshold >= 0.0 )
165 puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
167 puts( "i-E-value threshold : no threshold" )
169 if ( parse_descriptions )
170 puts( "parse descriptions : true" )
172 puts( "parse descriptions : false" )
175 puts( "ignore DUFs : true" )
177 puts( "ignore DUFs : false" )
179 if ( column_delimiter == "\t" )
180 puts( "column delimiter : TAB" )
182 puts( "column delimiter : " + column_delimiter )
184 if fs_e_value_threshold >= 0.0
185 puts( "E-value threshold : " + fs_e_value_threshold.to_s )
187 puts( "E-value threshold : no threshold" )
189 if !hmm_for_protein_output.empty?
190 puts( "HMM for proteins : " + hmm_for_protein_output )
193 puts( "Uniprot : " + uniprot )
204 fs_e_value_threshold,
205 hmm_for_protein_output,
208 Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
210 domain_counts = get_domain_counts()
214 puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
215 puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
217 puts( Util.draw_histogram( domain_counts, "#" ) )
219 Util.print_message( PRG_NAME, 'OK' )
226 # raises ArgumentError, IOError
233 fs_e_value_threshold,
234 hmm_for_protein_output,
239 Util.check_file_for_readability( inpath )
240 Util.check_file_for_writability( outpath )
242 hmmscan_parser = HmmscanParser.new( inpath )
243 results = hmmscan_parser.parse
245 uniprot_entries = nil
246 if !uniprot.empty? && !hmm_for_protein_output.empty?
247 uniprot_entries = read_uniprot( results, uniprot )
250 outfile = File.open( outpath, "a" )
259 hmmscan_results_per_protein = []
265 results.each do | r |
268 i_e_value = r.i_e_value
269 env_from = r.env_from
272 if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) &&
273 ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
275 outfile.print( query +
277 if ( get_descriptions )
278 outfile.print( desc +
281 outfile.print( model +
288 outfile.print( Constants::LINE_DELIMITER )
291 if !hmm_for_protein_output.empty?
292 if !prev_query.empty? && prev_query != query
293 if !hmmscan_results_per_protein.empty?
294 process_hmmscan_results_per_protein( hmmscan_results_per_protein,
295 fs_e_value_threshold,
296 hmm_for_protein_output,
300 hmmscan_results_per_protein.clear
305 if !AVOID_HHMS.include? r.model
306 hmmscan_results_per_protein << r
309 hmmscan_results_per_protein << r
313 if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
314 process_hmmscan_results_per_protein( hmmscan_results_per_protein,
315 fs_e_value_threshold,
316 hmm_for_protein_output,
327 if id =~ /(sp|tr)\|\S+\|(\S+)/
333 def read_uniprot( hmmscan_results, uniprot )
335 hmmscan_results.each do | r |
337 ids << process_id( r.query )
339 uniprot_parser = UniprotParser.new uniprot
340 uniprot_entries = uniprot_parser.parse ids
344 def count_model( model )
345 if ( @domain_counts.has_key?( model ) )
346 count = @domain_counts[ model ].to_i
348 @domain_counts[ model ] = count
350 @domain_counts[ model ] = 1
354 def process_hmmscan_results_per_protein( hmmscan_results_per_protein,
355 fs_e_value_threshold,
356 hmm_for_protein_output,
361 # filter according to i-Evalue threshold
362 # abort if fs Evalue too high
363 hmmscan_results_per_protein_filtered = []
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
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
380 # passed on protein E-value, failed in per domain E-values
384 hmmscan_results_per_protein_filtered.sort! { |r1,r2| r1.env_from <=> r2.env_from }
387 hmmscan_results_per_protein_filtered.each do | r |
388 if r.model == hmm_for_protein_output
394 s << own.query + "\t"
396 s << own.fs_e_value.to_s + "\t"
397 s << own.qlen.to_s + "\t"
399 s << hmmscan_results_per_protein_filtered.length.to_s + "\t"
400 hmmscan_results_per_protein_filtered.each do | r |
404 e = uniprot_entries[ process_id( own.query ) ]
405 if e != nil && e.de != nil
406 e.de.each { |i| s << i + " " }
412 if e != nil && e.gn != nil
413 e.gn.each { |i| s << i + " " }
421 overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
425 s << calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + "\t"
428 hmmscan_results_per_protein_filtered.each do | r |
431 s << make_interdomain_sequence( r.env_from - prev_r.env_to - 1 )
433 s << make_interdomain_sequence( r.env_from, false )
437 s << r.env_from.to_s << "-" << r.env_to.to_s
438 s << "|ie=" << r.i_e_value.to_s
439 s << "|ce=" << r.c_e_value.to_s
443 s << make_interdomain_sequence( own.qlen - prev_r.env_from, false )
448 def calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
451 hmmscan_results_per_protein_filtered.each do | r |
452 if r.model == hmm_for_protein_output
454 linkers << ( r.env_from - prev_r.env_to - 1 ).to_s + " "
462 def get_domain_counts()
463 return @domain_counts
466 def make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
469 hmmscan_results_per_protein_filtered.each do | r |
470 if r.model == hmm_for_protein_output
472 overview << hmm_for_protein_output
474 if ( r.env_from - prev_r.env_to - 1 ) <= LIMIT_FOR_CLOSE_DOMAINS
475 overview << "~" << hmm_for_protein_output
477 overview << "----" << hmm_for_protein_output
486 def make_interdomain_sequence( d, mark_short = true )
506 puts( " " + PRG_NAME + ".rb [options] <hmmscan outputfile> <outputfile>" )
508 puts( " options: -" + DELIMITER_OPTION + ": column delimiter for outputfile, default is TAB" )
509 puts( " -" + I_E_VALUE_THRESHOLD_OPTION + ": i-E-value threshold, default is no threshold" )
510 puts( " -" + PARSE_OUT_DESCRIPITION_OPTION + ": parse query description (in addition to query name)" )
511 puts( " -" + IGNORE_DUF_OPTION + ": ignore DUFs" )
512 puts( " -" + FS_E_VALUE_THRESHOLD_OPTION + ": E-value threshold for full protein sequences, only for protein summary" )
513 puts( " -" + HMM_FOR_PROTEIN_OUTPUT + ": HMM for protein summary" )