failed_seqs = Msa.new
passed_seqs = Msa.new
out_msa_pairs = nil
+ out_msa_distance_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
proteins_with_passing_domains = 0
proteins_with_failing_domains = 0
max_domain_copy_number_per_protein = -1
- max_domain_copy_number_sequence = ''
- failed_species_counts = Hash.new
- passed_species_counts = Hash.new
+ 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
next
end
-
sequence = $4
number = $10.to_i
out_of = $11.to_i
max_domain_copy_number_sequence = sequence
max_domain_copy_number_per_protein = number
end
- if ( ( ( e_value_threshold.to_f < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
- ( ( length_threshold.to_f <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
+ 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,
trim_name ,
add_species )
domain_pass_counter += 1
- count_species( sequence, passed_species_counts )
+
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 sequence == prev_sequence && ( ( ( e_value_threshold.to_f < 0.0 ) || ( prev_i_e_value <= e_value_threshold ) ) &&
- ( ( length_threshold.to_f <= 0 ) || ( ( prev_env_to - prev_env_from + 1 ) >= length_threshold.to_f ) ) )
- diff = env_from - prev_env_to
- if diff <= min_linker
+ if ( ( e_value_threshold < 0.0 ) || ( prev_i_e_value <= e_value_threshold ) ) &&
+ ( ( length_threshold <= 0 ) || ( ( prev_env_to - prev_env_from + 1 ) >= length_threshold.to_f ) )
+
+ if sequence != prev_sequence
+ prev_is_pair = false
+ end
+
+ if out_of == 1
+
+ if sequence == prev_sequence
+ puts "sequence == prev_sequence && out_of == 1"
+ exit
+ end
extract_domain( sequence,
- prev_number.to_s + "/" + number.to_s,
+ number,
out_of,
- prev_env_from,
+ env_from,
env_to,
in_msa,
- out_msa_pairs,
+ out_msa_singlets,
false,
true,
false,
false,
trim_name ,
add_species )
+
+ elsif sequence == prev_sequence
+
+ 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
+ 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 )
+ 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 )
+ end
+ prev_is_pair = false
+ end #######
+
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
- prev_sequence = sequence
- prev_number = number
- prev_env_from = env_from
- prev_env_to = env_to
- prev_i_e_value = i_e_value
- end
- 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
- count_species( sequence, failed_species_counts )
- if failed_seqs.find_by_name_start( sequence, true ).length < 1
- add_sequence( sequence, in_msa, failed_seqs )
- proteins_with_failing_domains += 1
+ 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
end
end
- end
- 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 domain_pass_counter < 1
+ error_msg = "no domain sequences were extracted"
+ raise StandardError, error_msg
+ end
- 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
+ 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
- io = MsaIO.new()
- w = FastaWriter.new()
- w.set_line_width( 60 )
- w.clean( true )
+ 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
- begin
- io.write_to_file( out_msa, outfile, w )
- rescue Exception
- error_msg = "could not write to \"" + outfile + "\""
- raise IOError, error_msg
- end
+ write_msa( out_msa, outfile )
+ write_msa( passed_seqs, passed_seqs_outfile )
+ write_msa( failed_seqs, failed_seqs_outfile )
- if out_msa_pairs
- begin
- io.write_to_file( out_msa_pairs, outfile+"_" + min_linker.to_s, w )
- rescue Exception
- error_msg = "could not write to \"" + outfile+"_" + min_linker.to_s + "\""
- raise IOError, error_msg
+ if out_msa_pairs
+ write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s )
end
- end
- begin
- io.write_to_file( passed_seqs, passed_seqs_outfile, w )
- rescue Exception
- error_msg = "could not write to \"" + passed_seqs_outfile + "\""
- raise IOError, error_msg
- end
+ if out_msa_singlets
+ write_msa( out_msa_singlets, outfile +"_singles" )
+ end
- begin
- io.write_to_file( failed_seqs, failed_seqs_outfile, w )
- rescue Exception
- error_msg = "could not write to \"" + failed_seqs_outfile + "\""
- raise IOError, error_msg
- end
+ if out_msa_distant_partners
+ write_msa( out_msa_distant_partners, outfile +"_singles" )
+ end
- log << ld
- log << "passing domains : " + domain_pass_counter.to_s + ld
- 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
- log << 'passing domains counts per species: ' << ld
- passed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld }
- log << ld
- log << 'failing domains counts per species: ' << ld
- failed_species_counts.each_pair { | species, count | log << "#{species}: #{count}" << ld }
- log << ld
- return domain_pass_counter
-
- end # parse
-
- private
-
- 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 )
+ log << ld
+ log << "passing domains : " + domain_pass_counter.to_s + ld
+ 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
- orig_name = seq.get_name
+ return domain_pass_counter
- seq.set_name( orig_name.split[ 0 ] )
+ end # parse
- 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
+ private
- 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 )
+ 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
- # 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
+ 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
- species = orig_name[ a .. b ]
- seq.set_name( seq.get_name + " " + species )
+ seq = in_msa.get_sequence( seqs[ 0 ] )
+ add_to_msa.add_sequence( seq )
end
- out_msa.add_sequence( seq )
+ # 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
- end
+ seq.set_name( orig_name.split[ 0 ] )
- def count_species( sequence, species_counts_map )
- species = get_species( sequence )
- if species != nil
- if !species_counts_map.has_key?( species )
- species_counts_map[ species ] = 1
- else
- species_counts_map[ species ] = species_counts_map[ species ] + 1
+ if add_position
+ seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
end
- end
- end
- def get_species( sequence_name )
- if sequence_name =~ /^.+_(.+)$/
- return $1
- else
- return nil
+ 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
- end
- def is_ignorable?( line )
- return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
- end
+ def is_ignorable?( line )
+ return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
+ end
- end # class HmmscanDomainExtractor
+ end # class HmmscanDomainExtractor
-end # module Evoruby
+ end # module Evoruby
git://source.jalview.org / jalview.git / commitdiff