add_domain_number_as_digit,
add_domain_number_as_letter,
trim_name,
+ add_species,
+ min_linker,
log )
Util.check_file_for_readability( hmmsearch_output )
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
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
if domain_id != target_name
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,
add_domain_number,
add_domain_number_as_digit,
add_domain_number_as_letter,
- trim_name )
+ 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
- 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
+
+ if 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 prev_sequence && sequence != prev_sequence
+ prev_is_pair = false
+ end
+
+ if out_of == 1
+
+ if rev_sequence && sequence == prev_sequence
+ puts "sequence == prev_sequence && out_of == 1"
+ exit
+ end
+ extract_domain( sequence,
+ number,
+ out_of,
+ env_from,
+ env_to,
+ in_msa,
+ out_msa_singlets,
+ false,
+ true,
+ false,
+ false,
+ trim_name ,
+ add_species )
+
+ elsif prev_sequence && 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
+
+ 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
+ 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"
log << Constants::LINE_DELIMITER
end
- io = MsaIO.new()
- w = FastaWriter.new()
- w.set_line_width( 60 )
- w.clean( true )
+ write_msa( out_msa, outfile )
+ write_msa( passed_seqs, passed_seqs_outfile )
+ write_msa( failed_seqs, failed_seqs_outfile )
- begin
- io.write_to_file( out_msa, outfile, w )
- rescue Exception
- error_msg = "could not write to \"" + outfile + "\""
- raise IOError, error_msg
+ if out_msa_pairs
+ write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s )
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
+ 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
+ if out_msa_distant_partners
+ write_msa( out_msa_distant_partners, outfile +"_dist" )
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 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 )
add_domain_number,
add_domain_number_as_digit,
add_domain_number_as_letter,
- trim_name )
- if ( number < 1 || out_of < 1 || number > out_of )
+ 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 )
+ 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
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 )
-
- seq.set_name( seq.get_name.split[ 0 ] )
-
+
+ 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
end
if out_of != 1
- if ( add_domain_number_as_digit )
+ if add_domain_number_as_digit
seq.set_name( seq.get_name + number.to_s )
- elsif ( add_domain_number_as_letter )
+ 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 )
+ elsif add_domain_number
seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
end
end
# raise StandardError, error_msg
# end
- out_msa.add_sequence( seq )
- end
-
- 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_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
- end
-
- def get_species( sequence_name )
- if sequence_name =~ /^.+_(.+)$/
- return $1
- else
- return nil
- end
+ out_msa.add_sequence( seq )
end
def is_ignorable?( line )
git://source.jalview.org / jalview.git / blobdiff