def initialize
end
+
+ def process_hmmscan_datas( hmmscan_datas,
+ in_msa,
+ add_position,
+ add_domain_number,
+ trim_name ,
+ add_species,
+ out_msa )
+
+ actual_out_of = hmmscan_datas.size
+
+ domain_pass_counter = 0;
+
+ hmmscan_datas.each_with_index do |hmmscan_data, index|
+ if hmmscan_data.number < ( index + 1 )
+ error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
+ raise StandardError, error_msg
+ end
+
+ extract_domain( hmmscan_data.seq_name,
+ index + 1,
+ actual_out_of,
+ hmmscan_data.env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa,
+ add_position,
+ add_domain_number,
+ trim_name ,
+ add_species )
+ domain_pass_counter += 1
+
+ # if passed_seqs.find_by_name_start( hmmscan_data.seq_name, true ).length < 1
+ # add_sequence( hmmscan_data.seq_name, in_msa, passed_seqs )
+ # proteins_with_passing_domains += 1
+ # end
+
+=begin
+ 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
+=end
+
+ end # each
+ domain_pass_counter
+ end # def process_hmmscan_data
+
+
# raises ArgumentError, IOError, StandardError
def parse( domain_id,
- hmmsearch_output,
+ hmmscan_output,
fasta_sequence_file,
outfile,
passed_seqs_outfile,
add_domain_number_as_digit,
add_domain_number_as_letter,
trim_name,
- add_species,
+ add_species,
+ min_linker,
log )
- Util.check_file_for_readability( hmmsearch_output )
+ Util.check_file_for_readability( hmmscan_output )
Util.check_file_for_readability( fasta_sequence_file )
Util.check_file_for_writability( outfile )
Util.check_file_for_writability( passed_seqs_outfile )
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 = ''
- 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 |
+ hmmscan_datas = Array.new
+
+
+ File.open( hmmscan_output ) do | file |
while line = file.gets
if !is_ignorable?( line ) && line =~ /^\S+\s+/
# 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
+ if domain_id != $1
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.to_f < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
- ( ( length_threshold.to_f <= 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 )
- 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
+
+ if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
+ ( ( length_threshold <= 0 ) || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
+ hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
+ if ( number > max_domain_copy_number_per_protein )
+ max_domain_copy_number_sequence = sequence
+ max_domain_copy_number_per_protein = number
end
- else
+ else # failed
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( " l=" + le.to_s )
log << " l=" + le.to_s
end
- print( Constants::LINE_DELIMITER )
- log << Constants::LINE_DELIMITER
+ print( ld )
+ log << ld
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
end
end
+
+ if number > out_of
+ error_msg = "number > out_of ! (this should not have happened)"
+ raise StandardError, error_msg
+ end
+
+ if number == out_of && !hmmscan_datas.empty?
+ domain_pass_counter += process_hmmscan_datas( hmmscan_datas,
+ in_msa,
+ add_position,
+ add_domain_number,
+ trim_name ,
+ add_species,
+ out_msa )
+
+ hmmscan_datas.clear
+ end
+
end
- end
- end
+ 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
+ raise IOError, error_msg
end
- log << Constants::LINE_DELIMITER
+ log << ld
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
+ log << ld
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
+ log << ld
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 + "_" + 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
- 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_to_msa.add_sequence( seq )
end
- # raises ArgumentError, StandardError
+
def extract_domain( sequence,
number,
out_of,
out_msa,
add_position,
add_domain_number,
- add_domain_number_as_digit,
- add_domain_number_as_letter,
trim_name,
- add_species )
- if ( number < 1 || out_of < 1 || number > out_of )
+ 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
+ raise StandardError, 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
+ raise StandardError, 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
+ raise IOError, error_msg
end
if seqs.length > 1
error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
- raise StandardError, error_msg
+ raise IOError, 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
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
-
- 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
-
+ if out_of != 1 && add_domain_number
+ seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
end
- # if ( seq.get_name.length > 10 )
- # error_msg = "sequence name [" + seq.get_name + "] is longer than 10 characters"
- # 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 )
end # class HmmscanDomainExtractor
+ class HmmsearchData
+ def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
+ @seq_name = seq_name
+ @number = number
+ @out_of = out_of
+ @env_from = env_from
+ @env_to = env_to
+ @i_e_value = i_e_value
+ end
+ attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value
+ end
+
end # module Evoruby
git://source.jalview.org / jalview.git / blobdiff