+++ /dev/null
-#
-# = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class
-#
-# Copyright:: Copyright (C) 2012 Christian M. Zmasek
-# License:: GNU Lesser General Public License (LGPL)
-#
-# $Id: $
-
-
-require 'lib/evo/util/constants'
-require 'lib/evo/msa/msa_factory'
-require 'lib/evo/io/msa_io'
-require 'lib/evo/io/writer/fasta_writer'
-require 'lib/evo/io/parser/fasta_parser'
-
-
-module Evoruby
-
- class HmmscanDomainExtractor
-
- TRIM_BY = 2
-
- def initialize
- end
-
- # raises ArgumentError, IOError, StandardError
- def parse( domain_id,
- hmmsearch_output,
- fasta_sequence_file,
- outfile,
- passed_seqs_outfile,
- failed_seqs_outfile,
- e_value_threshold,
- length_threshold,
- add_position,
- add_domain_number,
- add_domain_number_as_digit,
- add_domain_number_as_letter,
- trim_name,
- add_species,
- min_linker,
- log )
-
- Util.check_file_for_readability( hmmsearch_output )
- Util.check_file_for_readability( fasta_sequence_file )
- Util.check_file_for_writability( outfile )
- Util.check_file_for_writability( passed_seqs_outfile )
- Util.check_file_for_writability( failed_seqs_outfile )
-
- in_msa = nil
- factory = MsaFactory.new()
- in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )
-
- if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
- error_msg = "could not find fasta sequences in " + fasta_sequence_file
- raise IOError, error_msg
- end
-
- out_msa = Msa.new
-
- failed_seqs = Msa.new
- passed_seqs = Msa.new
- out_msa_pairs = nil
- out_msa_distant_partners = nil
- out_msa_singlets = nil
- if min_linker
- out_msa_pairs = Msa.new
- out_msa_distant_partners = Msa.new
- out_msa_singlets = Msa.new
- end
-
- ld = Constants::LINE_DELIMITER
-
- domain_pass_counter = 0
- domain_fail_counter = 0
- singlets_counter = 0
- distant_pairs_counter = 0
- close_pairs_counter = 0
- proteins_with_passing_domains = 0
- proteins_with_failing_domains = 0
- max_domain_copy_number_per_protein = -1
- max_domain_copy_number_sequence = ""
-
- prev_sequence = nil
- prev_number = nil
- prev_env_from = nil
- prev_env_to = nil
- # prev_i_e_value = nil
- prev_is_pair = false
-
- File.open( hmmsearch_output ) do | file |
- while line = file.gets
- if !is_ignorable?( line ) && line =~ /^\S+\s+/
-
- # tn acc tlen query acc qlen Evalue score bias # of c-E i-E score bias hf ht af at ef et acc desc
- # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
- 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+(.*)/
-
- target_name = $1
- if domain_id != target_name
- next
- end
-
- sequence = $4
- number = $10.to_i
- out_of = $11.to_i
- env_from = $20.to_i
- env_to = $21.to_i
- i_e_value = $13.to_f
- if ( number > max_domain_copy_number_per_protein )
- max_domain_copy_number_sequence = sequence
- max_domain_copy_number_per_protein = number
- end
- if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
- ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
-
- extract_domain( sequence,
- number,
- out_of,
- env_from,
- env_to,
- in_msa,
- out_msa,
- add_position,
- add_domain_number,
- add_domain_number_as_digit,
- add_domain_number_as_letter,
- trim_name ,
- add_species )
- domain_pass_counter += 1
-
- if passed_seqs.find_by_name_start( sequence, true ).length < 1
- add_sequence( sequence, in_msa, passed_seqs )
- proteins_with_passing_domains += 1
- end
-
- if min_linker
- if out_of == 1
- extract_domain( sequence,
- number,
- out_of,
- env_from,
- env_to,
- in_msa,
- out_msa_singlets,
- false,
- true,
- false,
- false,
- trim_name,
- add_species )
- singlets_counter += 1
- elsif prev_sequence
- if sequence != prev_sequence
- prev_is_pair = false
- else
- if ( env_from - prev_env_to ) <= min_linker
- extract_domain( sequence,
- prev_number.to_s + "+" + number.to_s,
- out_of,
- prev_env_from,
- env_to,
- in_msa,
- out_msa_pairs,
- false,
- true,
- false,
- false,
- trim_name,
- add_species )
- prev_is_pair = true
- close_pairs_counter += 2
- else
- if !prev_is_pair
- extract_domain( sequence,
- prev_number,
- out_of,
- prev_env_from,
- prev_env_to,
- in_msa,
- out_msa_distant_partners,
- false,
- true,
- false,
- false,
- trim_name,
- add_species )
- distant_pairs_counter += 1
- end
- if number == out_of
- extract_domain( sequence,
- number,
- out_of,
- env_from,
- env_to,
- in_msa,
- out_msa_distant_partners,
- false,
- true,
- false,
- false,
- trim_name,
- add_species )
- distant_pairs_counter += 1
- end
- prev_is_pair = false
- end
- end # sequence != prev_sequence else
- end
- prev_sequence = sequence
- prev_number = number
- prev_env_from = env_from
- prev_env_to = env_to
- #prev_i_e_value = i_e_value
- end # if min_linker
-
- else
- print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
- log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
- if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
- print( " iE=" + i_e_value.to_s )
- log << " iE=" + i_e_value.to_s
- end
- if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
- le = env_to - env_from + 1
- print( " l=" + le.to_s )
- log << " l=" + le.to_s
- end
- print( Constants::LINE_DELIMITER )
- log << Constants::LINE_DELIMITER
- domain_fail_counter += 1
-
- if failed_seqs.find_by_name_start( sequence, true ).length < 1
- add_sequence( sequence, in_msa, failed_seqs )
- proteins_with_failing_domains += 1
- end
-
- end
- end # if !is_ignorable?( line ) && line =~ /^\S+\s+/
- end # while line = file.gets
- end # File.open( hmmsearch_output ) do | file |
-
- if domain_pass_counter < 1
- error_msg = "no domain sequences were extracted"
- raise StandardError, error_msg
- end
-
- log << Constants::LINE_DELIMITER
- puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
- log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
- log << Constants::LINE_DELIMITER
-
- if ( max_domain_copy_number_per_protein > 1 )
- puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
- log << "First protein with this copy number: " + max_domain_copy_number_sequence
- log << Constants::LINE_DELIMITER
- end
-
- write_msa( out_msa, outfile )
- write_msa( passed_seqs, passed_seqs_outfile )
- write_msa( failed_seqs, failed_seqs_outfile )
-
- if out_msa_pairs
- write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s )
- end
-
- if out_msa_singlets
- write_msa( out_msa_singlets, outfile +"_singles" )
- end
-
- if out_msa_distant_partners
- write_msa( out_msa_distant_partners, outfile + "_" + min_linker.to_s + "_isolated" );
- end
-
-
- log << ld
- log << "passing domains : " + domain_pass_counter.to_s + ld
- if ( min_linker )
- log << "single domains : " + singlets_counter.to_s + ld
- log << "domains in close pairs : " + close_pairs_counter.to_s + ld
- log << "isolated domains : " + distant_pairs_counter.to_s + ld
- end
- log << "failing domains : " + domain_fail_counter.to_s + ld
- log << "proteins with passing domains: " + proteins_with_passing_domains.to_s + ld
- log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
- log << ld
-
- return domain_pass_counter
-
- end # parse
-
-
- private
-
- def write_msa( msa, filename )
- io = MsaIO.new()
- w = FastaWriter.new()
- w.set_line_width( 60 )
- w.clean( true )
- begin
- io.write_to_file( msa, filename, w )
- rescue Exception
- error_msg = "could not write to \"" + filename + "\""
- raise IOError, error_msg
- end
- end
-
-
- def add_sequence( sequence_name, in_msa, add_to_msa )
- seqs = in_msa.find_by_name_start( sequence_name, true )
- if ( seqs.length < 1 )
- error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
- raise StandardError, error_msg
- end
- if ( seqs.length > 1 )
- error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
- raise StandardError, error_msg
- end
- seq = in_msa.get_sequence( seqs[ 0 ] )
- add_to_msa.add_sequence( seq )
- end
-
- # raises ArgumentError, StandardError
- def extract_domain( sequence,
- number,
- out_of,
- seq_from,
- seq_to,
- in_msa,
- out_msa,
- add_position,
- add_domain_number,
- add_domain_number_as_digit,
- add_domain_number_as_letter,
- trim_name,
- add_species )
- if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
- error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
- raise ArgumentError, error_msg
- end
- if seq_from < 1 || seq_to < 1 || seq_from >= seq_to
- error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
- raise ArgumentError, error_msg
- end
- seqs = in_msa.find_by_name_start( sequence, true )
- if seqs.length < 1
- error_msg = "sequence \"" + sequence + "\" not found in sequence file"
- raise StandardError, error_msg
- end
- if seqs.length > 1
- error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
- raise StandardError, error_msg
- end
- # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
- seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )
-
- orig_name = seq.get_name
-
- seq.set_name( orig_name.split[ 0 ] )
-
- if add_position
- seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
- end
-
- if trim_name
- seq.set_name( seq.get_name[ 0, seq.get_name.length - TRIM_BY ] )
- end
-
- if out_of != 1
- if add_domain_number_as_digit
- seq.set_name( seq.get_name + number.to_s )
- elsif add_domain_number_as_letter
- if number > 25
- error_msg = 'too many identical domains per sequence, cannot use letters to distinguish them'
- raise StandardError, error_msg
- end
- seq.set_name( seq.get_name + ( number + 96 ).chr )
- elsif add_domain_number
- seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
- end
- end
-
- # if ( seq.get_name.length > 10 )
- # error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters"
- # raise StandardError, error_msg
- # end
-
- if add_species
- a = orig_name.rindex "["
- b = orig_name.rindex "]"
- unless a && b
- error_msg = "species not found in " + orig_name
- raise StandardError, error_msg
- end
- species = orig_name[ a .. b ]
- seq.set_name( seq.get_name + " " + species )
- end
- out_msa.add_sequence( seq )
- end
-
- def is_ignorable?( line )
- return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
- end
-
- end # class HmmscanDomainExtractor
-
-end # module Evoruby
-
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