LENGTH_THRESHOLD_OPTION = 'l'
ADD_POSITION_OPTION = 'p'
ADD_DOMAIN_NUMBER_OPTION = 'd'
- ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT = 'dd'
- ADD_DOMAIN_NUMBER_OPTION_AS_LETTER = 'dl'
ADD_SPECIES = 's'
MIN_LINKER_OPT = 'ml'
- TRIM_OPTION = 't'
LOG_FILE_SUFFIX = '_domain_seq_extr.log'
PASSED_SEQS_SUFFIX = '_domain_seq_extr_passed'
FAILED_SEQS_SUFFIX = '_domain_seq_extr_failed'
allowed_opts.push( ADD_POSITION_OPTION )
allowed_opts.push( ADD_DOMAIN_NUMBER_OPTION )
allowed_opts.push( LENGTH_THRESHOLD_OPTION )
- allowed_opts.push( ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT )
- allowed_opts.push( ADD_DOMAIN_NUMBER_OPTION_AS_LETTER )
- allowed_opts.push( TRIM_OPTION )
allowed_opts.push( ADD_SPECIES )
allowed_opts.push( MIN_LINKER_OPT )
add_position = true
end
- trim = false
- if ( cla.is_option_set?( TRIM_OPTION ) )
- trim = true
- end
-
add_domain_number = false
- add_domain_number_as_letter = false
- add_domain_number_as_digit = false
-
if ( cla.is_option_set?( ADD_DOMAIN_NUMBER_OPTION ) )
add_domain_number = true
end
- if ( cla.is_option_set?( ADD_DOMAIN_NUMBER_OPTION_AS_LETTER ) )
- add_domain_number_as_letter = true
- end
- if ( cla.is_option_set?( ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT ) )
- add_domain_number_as_digit = true
- end
add_species = false
if cla.is_option_set? ADD_SPECIES
add_species = true
end
- if ( add_domain_number_as_letter && add_domain_number_as_digit )
- puts( "attempt to add domain number as letter and digit at the same time" )
- print_help
- exit( -1 )
- end
-
e_value_threshold = -1.0
if ( cla.is_option_set?( E_VALUE_THRESHOLD_OPTION ) )
begin
puts( "Length threshold : no threshold" )
log << "Length threshold : no threshold" + ld
end
-
- if ( trim )
- puts( "Trim last 2 chars : true" )
- log << "Trim last 2 chars : true" + ld
- else
- puts( "Trim names : false" )
- log << "Trim names : false" + ld
- end
-
if ( min_linker )
puts( "Min linker : " + min_linker.to_s )
log << "Min linker : " + min_linker.to_s + ld
log << "Add positions (rel to complete seq) to extracted domains: false" + ld
end
- if ( add_domain_number || add_domain_number_as_digit || add_domain_number_as_letter )
+ if ( add_domain_number )
puts( "Add numbers to extracted domains (in case of more than one domain per complete seq): true" )
log << "Add numbers to extracted domains (in case of more than one domain per complete seq): true" + ld
else
length_threshold,
add_position,
add_domain_number,
- add_domain_number_as_digit,
- add_domain_number_as_letter,
- trim,
add_species,
min_linker,
log )
rescue ArgumentError, IOError => e
+ puts e.backtrace
Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
rescue Exception => e
puts( " -" + LENGTH_THRESHOLD_OPTION + "=<i>: length threshold, default is no threshold" )
puts( " -" + ADD_POSITION_OPTION + ": to add positions (rel to complete seq) to extracted domains" )
puts( " -" + ADD_DOMAIN_NUMBER_OPTION + ": to add numbers to extracted domains (in case of more than one domain per complete seq) (example \"domain~2-3\")" )
- puts( " -" + ADD_DOMAIN_NUMBER_OPTION_AS_DIGIT + ": to add numbers to extracted domains as digit (example \"domain2\")" )
- puts( " -" + ADD_DOMAIN_NUMBER_OPTION_AS_LETTER + ": to add numbers to extracted domains as letter (example \"domaina\")" )
- puts( " -" + TRIM_OPTION + ": to remove the last 2 characters from sequence names" )
puts( " -" + ADD_SPECIES + ": to add species [in brackets]" )
puts( " -" + MIN_LINKER_OPT + "=<i>: to extract pairs of same domains with a distance inbetween shorter than a given value" )
puts()
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,
- out_msa_pairs,
- out_msa_isolated,
- 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,
- 1,
- hmmscan_data.env_from,
- hmmscan_data.env_to,
- in_msa,
- out_msa_singles,
- add_position,
- add_domain_number,
- trim_name ,
- add_species )
- else
- first = index == 0
- last = index == hmmscan_datas.length - 1
- next_env_from = hmmscan_datas[ index + 1 ].env_from
- env_to = hmmscan_data.env_to
- env_from = hmmscan_data.env_from
- prev_env_to = hmmscan_datas[ index - 1 ].env_to
-
-
- 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 &&
- 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,
- 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 )
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
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
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
in_msa,
add_position,
add_domain_number,
- trim_name ,
add_species,
out_msa,
out_msa_singles,
- passed_seqs )
+ out_msa_pairs,
+ out_msa_isolated,
+ passed_seqs,
+ min_linker )
hmmscan_datas.clear
end
write_msa( out_msa_singles, outfile +"_singles" )
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" );
end
log << "isolated domains : " + distant_pairs_counter.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 passing domains: " + passed_seqs.get_number_of_seqs.to_s + ld
log << "proteins with failing domains: " + proteins_with_failing_domains.to_s + ld
log << ld
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,
+ passed_seqs,
+ min_linker )
+
+ 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,
+ 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 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
+ # next_env_from = hmmscan_datas[ index + 1 ].env_from
+ # env_to = hmmscan_data.env_to
+ # env_from = hmmscan_data.env_from
+ # prev_env_to = hmmscan_datas[ index - 1 ].env_to
+
+
+ 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 ) && ( last && 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
+ domain_pass_counter
+ 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
git://source.jalview.org / jalview.git / commitdiff