class HmmscanDomainExtractor
- TRIM_BY = 2
-
def initialize
end
-
- def process_hmmscan_datas( hmmscan_datas,
- in_msa,
- add_position,
- add_domain_number,
- trim_name ,
- add_species,
- out_msa,
- out_msa_singles,
- passed_seqs )
-
- 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 )
- end
-
- if actual_out_of == 1
- extract_domain( hmmscan_data.seq_name,
- index + 1,
- actual_out_of,
- hmmscan_data.env_from,
- hmmscan_data.env_to,
- in_msa,
- out_msa_singles,
- add_position,
- add_domain_number,
- trim_name ,
- add_species )
- else
-
- if (( first && next_env_from - env_to >= min_linker )
- ||
- ( last && env_from - prev_env_to >= min_linker )
- ||
- ( !first && !last && ( next_env_from - env_to >= min_linker ) && ( last && env_from - prev_env_to >= min_linker ) ))
-
-
-
- elsif !first && ( 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 )
- end
- 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,
hmmscan_output,
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( 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_isolated = nil
out_msa_singles = nil
if min_linker
out_msa_pairs = Msa.new
- out_msa_distant_partners = Msa.new
+ out_msa_isolated = Msa.new
out_msa_singles = Msa.new
end
domain_pass_counter = 0
domain_fail_counter = 0
- singlets_counter = 0
- distant_pairs_counter = 0
- close_pairs_counter = 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 = Array.new
-
File.open( hmmscan_output ) do | file |
while line = file.gets
if !is_ignorable?( line ) && line =~ /^\S+\s+/
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 ) )
+ ( ( 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
print( ld )
log << ld
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
if number > out_of
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,
- out_msa_singles,
- passed_seqs )
-
+ 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
end
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_singles
- write_msa( out_msa_singles, outfile +"_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
log << ld
- log << "passing domains : " + domain_pass_counter.to_s + 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 << "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
end
- log << "failing domains : " + domain_fail_counter.to_s + ld
- log << "proteins with passing domains: " + passed_seqs.length.to_s + ld
- log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
+ 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
add_to_msa.add_sequence( seq )
end
+ 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 )
+
+ actual_out_of = hmmscan_datas.size
+
+ 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,
+ add_species )
+
+ if min_linker
+ if actual_out_of == 1
+ extract_domain( hmmscan_data.seq_name,
+ 1,
+ 1,
+ hmmscan_data.env_from,
+ hmmscan_data.env_to,
+ in_msa,
+ out_msa_singles,
+ add_position,
+ add_domain_number,
+ add_species )
+ 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( hmmscan_data.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 )
+
+ elsif !first
+ extract_domain( hmmscan_data.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 )
+ end
+ end
+ end
+ end # each
+ end # def process_hmmscan_data
def extract_domain( sequence,
number,
out_msa,
add_position,
add_domain_number,
- 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
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 && add_domain_number
seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
end
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