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
out_msa_pairs = 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_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
max_domain_copy_number_per_protein = -1
max_domain_copy_number_sequence = ""
- hmmscan_datas = Array.new
+ hmmscan_datas = []
- File.open( hmmscan_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
- if domain_id != $1
- 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 ( ( ( 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
+ if number > out_of
+ error_msg = "number > out_of ! (this should not have happened)"
+ raise StandardError, error_msg
+ end
- if number > out_of
- error_msg = "number > out_of ! (this should not have happened)"
+ 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
+ error_msg = "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 )
- 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
- error_msg = "this should not have happened"
- raise StandardError, error_msg
- end
- 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
+ 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
- end # while line = file.gets
- end # File.open( hmmsearch_output ) do | file |
-
-
+ hmmscan_datas.clear
+ end
+ end
if domain_pass_counter < 1
error_msg = "no domain sequences were extracted"
end
if out_msa_singles
- write_msa( out_msa_singles, outfile +"_singles" + ".fasta")
+ write_msa( out_msa_singles, outfile +"_singles.fasta")
end
if out_msa_isolated
- write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated" + ".fasta");
+ 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 : " + out_msa_singles.get_number_of_seqs.to_s + ld
- log << "domains in close pairs : " + out_msa_pairs.get_number_of_seqs.to_s + ld
- log << "isolated domains : " + out_msa_isolated.get_number_of_seqs.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 : " + passed_seqs.get_number_of_seqs.to_s + ld
- log << "proteins with no passing domains: " + proteins_with_failing_domains.to_s + ld
+
log << ld
return domain_pass_counter
out_msa_singles,
out_msa_pairs,
out_msa_isolated,
- min_linker )
+ 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 )
raise StandardError, error_msg
end
- extract_domain( hmmscan_data.seq_name,
+ seq_name = hmmscan_data.seq_name
+
+ extract_domain( seq_name,
index + 1,
actual_out_of,
hmmscan_data.env_from,
if min_linker
if actual_out_of == 1
- extract_domain( hmmscan_data.seq_name,
+ extract_domain( seq_name,
1,
1,
hmmscan_data.env_from,
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
( !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( hmmscan_data.seq_name,
+ extract_domain( seq_name,
index + 1,
actual_out_of,
hmmscan_data.env_from,
add_position,
add_domain_number,
add_species )
+ saw_isolated = true
elsif !first
- extract_domain( hmmscan_data.seq_name,
+ extract_domain( seq_name,
index.to_s + "+" + ( index + 1 ).to_s,
actual_out_of,
hmmscan_datas[ index - 1 ].env_from,
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,
git://source.jalview.org / jalview.git / blobdiff