require 'lib/evo/io/msa_io'
require 'lib/evo/io/writer/fasta_writer'
require 'lib/evo/io/parser/fasta_parser'
+require 'lib/evo/io/parser/hmmscan_parser'
+
module Evoruby
class HmmscanDomainExtractor
- TRIM_BY = 2
-
def initialize
end
# raises ArgumentError, IOError, StandardError
def parse( domain_id,
- hmmsearch_output,
+ hmmscan_output,
fasta_sequence_file,
outfile,
passed_seqs_outfile,
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( hmmscan_output )
Util.check_file_for_readability( fasta_sequence_file )
- Util.check_file_for_writability( outfile )
+ Util.check_file_for_writability( outfile + ".fasta" )
Util.check_file_for_writability( passed_seqs_outfile )
Util.check_file_for_writability( failed_seqs_outfile )
failed_seqs = Msa.new
passed_seqs = Msa.new
out_msa_pairs = nil
- out_msa_distant_partners = nil
- out_msa_singlets = nil
+ out_msa_isolated = nil
+ out_msa_singles = nil
+ out_msa_single_domains_protein_seqs = nil
+ out_msa_close_pairs_protein_seqs = nil
+ out_msa_close_pairs_only_protein_seqs = nil
+ out_msa_isolated_protein_seqs = nil
+ out_msa_isolated_only_protein_seqs = nil
+ out_msa_isolated_and_close_pair_protein_seqs = nil
if min_linker
out_msa_pairs = Msa.new
- out_msa_distant_partners = Msa.new
- out_msa_singlets = Msa.new
+ out_msa_isolated = Msa.new
+ out_msa_singles = Msa.new
+ out_msa_single_domains_protein_seqs = Msa.new
+ out_msa_close_pairs_protein_seqs = Msa.new
+ out_msa_close_pairs_only_protein_seqs = Msa.new
+ out_msa_isolated_protein_seqs = Msa.new
+ out_msa_isolated_only_protein_seqs = Msa.new
+ out_msa_isolated_and_close_pair_protein_seqs = 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
+ hmmscan_datas = []
- File.open( hmmsearch_output ) do | file |
- while line = file.gets
- if !is_ignorable?( line ) && line =~ /^\S+\s+/
+ hmmscan_parser = HmmscanParser.new( hmmscan_output )
+ results = hmmscan_parser.parse
- # 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+(.*)/
+ results.each do | r |
+ if domain_id != r.model
+ next
+ end
- target_name = $1
- if domain_id != target_name
- next
- end
+ sequence = r.query
+ number = r.number
+ out_of = r.out_of
+ env_from = r.env_from
+ env_to = r.env_to
+ i_e_value = r.i_e_value
+
+ 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 # 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( " 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( ld )
+ log << ld
+ domain_fail_counter += 1
+ 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
+ if number > out_of
+ error_msg = "number > out_of ! (this should not have happened)"
+ raise StandardError, error_msg
+ end
+ if number == out_of
+ if !hmmscan_datas.empty?
+ process_hmmscan_datas( hmmscan_datas,
+ in_msa,
+ add_position,
+ add_domain_number,
+ add_species,
+ out_msa,
+ out_msa_singles,
+ out_msa_pairs,
+ out_msa_isolated,
+ min_linker,
+ out_msa_single_domains_protein_seqs,
+ out_msa_close_pairs_protein_seqs,
+ out_msa_close_pairs_only_protein_seqs,
+ out_msa_isolated_protein_seqs,
+ out_msa_isolated_only_protein_seqs,
+ out_msa_isolated_and_close_pair_protein_seqs )
+ domain_pass_counter += hmmscan_datas.length
+ if passed_seqs.find_by_name_start( sequence, true ).length < 1
+ add_sequence( sequence, in_msa, passed_seqs )
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
-
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
end
- end # if !is_ignorable?( line ) && line =~ /^\S+\s+/
- end # while line = file.gets
- end # File.open( hmmsearch_output ) do | file |
+ else
+ if failed_seqs.find_by_name_start( sequence, true ).length < 1
+ add_sequence( sequence, in_msa, failed_seqs )
+ proteins_with_failing_domains += 1
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end
+ hmmscan_datas.clear
+ end
+ end
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
- write_msa( out_msa, outfile )
+ write_msa( out_msa, outfile + ".fasta" )
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 )
+ write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta")
end
- if out_msa_singlets
- write_msa( out_msa_singlets, outfile +"_singles" )
+ if out_msa_singles
+ write_msa( out_msa_singles, outfile +"_singles.fasta")
end
- if out_msa_distant_partners
- write_msa( out_msa_distant_partners, outfile + "_" + min_linker.to_s + "_isolated" );
+ if out_msa_isolated
+ write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated.fasta");
end
+ if out_msa_single_domains_protein_seqs
+ write_msa( out_msa_single_domains_protein_seqs, outfile +"_proteins_with_singles.fasta" )
+ end
+
+ if out_msa_close_pairs_protein_seqs
+ write_msa( out_msa_close_pairs_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_close_pairs.fasta" )
+ end
+
+ if out_msa_close_pairs_only_protein_seqs
+ write_msa( out_msa_close_pairs_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_close_pairs_only.fasta" )
+ end
+
+ if out_msa_isolated_protein_seqs
+ write_msa( out_msa_isolated_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains.fasta" )
+ end
+
+ if out_msa_isolated_only_protein_seqs
+ write_msa( out_msa_isolated_only_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_domains_only.fasta" )
+ end
+
+ if out_msa_isolated_and_close_pair_protein_seqs
+ write_msa( out_msa_isolated_and_close_pair_protein_seqs, outfile + "_" + min_linker.to_s + "_proteins_with_isolated_and_close_pairs.fasta" )
+ end
+
+ if min_linker
+ if ( out_msa_single_domains_protein_seqs.get_number_of_seqs +
+ out_msa_close_pairs_only_protein_seqs.get_number_of_seqs +
+ out_msa_isolated_only_protein_seqs.get_number_of_seqs +
+ out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs ) != passed_seqs.get_number_of_seqs
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ 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
+ log << "passing domains : " + domain_pass_counter.to_s + ld
+ log << "failing domains : " + domain_fail_counter.to_s + ld
+ log << "input proteins : " + in_msa.get_number_of_seqs.to_s + ld
+ log << "proteins with passing domains : " + passed_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with no passing domains : " + proteins_with_failing_domains.to_s + ld
+ if min_linker
+ log << "min linker length : " + min_linker.to_s + ld
+ log << "single domains : " + out_msa_singles.get_number_of_seqs.to_s + ld
+ log << "domains in close pairs : " + (2 * out_msa_pairs.get_number_of_seqs).to_s + ld
+ log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.to_s + ld
+ log << "proteins wih single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins wih close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins wih close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins wih isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins wih isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins wih close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.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
add_to_msa.add_sequence( seq )
end
- # raises ArgumentError, StandardError
+ def process_hmmscan_datas( hmmscan_datas,
+ in_msa,
+ add_position,
+ add_domain_number,
+ add_species,
+ out_msa,
+ out_msa_singles,
+ out_msa_pairs,
+ out_msa_isolated,
+ min_linker,
+ out_msa_single_domains_protein_seqs,
+ out_msa_close_pairs_protein_seqs,
+ out_msa_close_pairs_only_protein_seqs,
+ out_msa_isolated_protein_seqs,
+ out_msa_isolated_only_protein_seqs,
+ out_msa_isolated_and_close_pair_protein_seqs )
+
+ actual_out_of = hmmscan_datas.size
+ saw_close_pair = false
+ saw_isolated = false
+
+ seq_name = ""
+ prev_seq_name = nil
+
+ 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
+
+ seq_name = hmmscan_data.seq_name
+
+ extract_domain( seq_name,
+ index + 1,
+ actual_out_of,
+ hmmscan_data.env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa,
+ add_position,
+ add_domain_number,
+ add_species )
+
+ if min_linker
+ if actual_out_of == 1
+ extract_domain( seq_name,
+ 1,
+ 1,
+ hmmscan_data.env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa_singles,
+ add_position,
+ add_domain_number,
+ add_species )
+ if out_msa_single_domains_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_single_domains_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+
+ else
+ first = index == 0
+ last = index == hmmscan_datas.length - 1
+
+ if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) ) ||
+ ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
+ ( !first && !last && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
+ ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )
+
+ extract_domain( seq_name,
+ index + 1,
+ actual_out_of,
+ hmmscan_data.env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa_isolated,
+ add_position,
+ add_domain_number,
+ add_species )
+ saw_isolated = true
+
+ elsif !first
+ extract_domain( seq_name,
+ index.to_s + "+" + ( index + 1 ).to_s,
+ actual_out_of,
+ hmmscan_datas[ index - 1 ].env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa_pairs,
+ add_position,
+ add_domain_number,
+ add_species )
+ saw_close_pair = true
+ end
+ end
+ end
+ if prev_seq_name && prev_seq_name != seq_name
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ prev_seq_name = seq_name
+ end # each
+ if saw_isolated
+ if out_msa_isolated_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_isolated_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end
+ if saw_close_pair
+ if out_msa_close_pairs_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_close_pairs_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end
+ if saw_close_pair && saw_isolated
+ if out_msa_isolated_and_close_pair_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_isolated_and_close_pair_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ elsif saw_close_pair
+ if out_msa_close_pairs_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_close_pairs_only_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ elsif saw_isolated
+ if out_msa_isolated_only_protein_seqs.find_by_name_start( seq_name, true ).length < 1
+ add_sequence( seq_name, in_msa, out_msa_isolated_only_protein_seqs )
+ else
+ error_msg = "this should not have happened"
+ raise StandardError, error_msg
+ end
+ end
+ end # def process_hmmscan_data
+
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.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
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 )
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
+ 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
-
if add_species
a = orig_name.rindex "["
b = orig_name.rindex "]"
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