#
# = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class
#
-# Copyright:: Copyright (C) 2012 Christian M. Zmasek
-# License:: GNU Lesser General Public License (LGPL)
+# Copyright:: Copyright (C) 2017 Christian M. Zmasek
+# License:: GNU Lesser General Public License (LGPL)
#
-# $Id: $
-
+# Last modified: 2017/02/20
require 'lib/evo/util/constants'
require 'lib/evo/msa/msa_factory'
require 'lib/evo/io/parser/fasta_parser'
require 'lib/evo/io/parser/hmmscan_parser'
-
-
module Evoruby
-
class HmmscanDomainExtractor
- ADD_TO_CLOSE_PAIRS = 20
-
+ ADD_TO_CLOSE_PAIRS = 0
def initialize
end
# raises ArgumentError, IOError, StandardError
def parse( domain_id,
- hmmscan_output,
- fasta_sequence_file,
- outfile,
- passed_seqs_outfile,
- failed_seqs_outfile,
- e_value_threshold,
- length_threshold,
- add_position,
- add_domain_number,
- add_species,
- min_linker,
- log )
+ hmmscan_output,
+ fasta_sequence_file,
+ outfile,
+ passed_seqs_outfile,
+ failed_seqs_outfile,
+ e_value_threshold,
+ length_threshold,
+ add_position,
+ add_domain_number,
+ add_species,
+ min_linker,
+ log )
Util.check_file_for_readability( hmmscan_output )
Util.check_file_for_readability( fasta_sequence_file )
ld = Constants::LINE_DELIMITER
- domain_pass_counter = 0
- domain_fail_counter = 0
- proteins_with_failing_domains = 0
+ domain_pass_counter = 0
+ domain_fail_counter = 0
+ passing_domains_per_protein = 0
+ proteins_with_failing_domains = 0
+ domain_not_present_counter = 0
+ protein_counter = 1
max_domain_copy_number_per_protein = -1
max_domain_copy_number_sequence = ""
+ passing_target_length_sum = 0
+ overall_target_length_sum = 0
+ overall_target_length_min = 10000000
+ overall_target_length_max = -1
+ passing_target_length_min = 10000000
+ passing_target_length_max = -1
+
+ overall_target_ie_min = 10000000
+ overall_target_ie_max = -1
+ passing_target_ie_min = 10000000
+ passing_target_ie_max = -1
hmmscan_datas = []
hmmscan_parser = HmmscanParser.new( hmmscan_output )
results = hmmscan_parser.parse
+ prev_query = nil
+ saw_target = false
+
results.each do | r |
+
+ if ( prev_query != nil ) && ( r.query != prev_query )
+ protein_counter += 1
+ passing_domains_per_protein = 0
+ if !saw_target
+ log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld
+ domain_not_present_counter += 1
+ end
+ saw_target = false
+ end
+
+ prev_query = r.query
+
if domain_id != r.model
next
end
+ saw_target = true
+
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
+ prev_query = r.query
+
+ length = 1 + env_to - env_from
+
+ overall_target_length_sum += length
+ if length > overall_target_length_max
+ overall_target_length_max = length
+ end
+ if length < overall_target_length_min
+ overall_target_length_min = length
+ end
+
+ if i_e_value > overall_target_ie_max
+ overall_target_ie_max = i_e_value
+ end
+ if i_e_value < overall_target_ie_min
+ overall_target_ie_min = i_e_value
+ 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 ) )
+ ( ( length_threshold <= 0 ) || ( length >= 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 )
+ passing_target_length_sum += length
+ passing_domains_per_protein += 1
+ if length > passing_target_length_max
+ passing_target_length_max = length
+ end
+ if length < passing_target_length_min
+ passing_target_length_min = length
+ end
+ if i_e_value > passing_target_ie_max
+ passing_target_ie_max = i_e_value
+ end
+ if i_e_value < passing_target_ie_min
+ passing_target_ie_min = i_e_value
+ end
+ if ( passing_domains_per_protein > max_domain_copy_number_per_protein )
max_domain_copy_number_sequence = sequence
- max_domain_copy_number_per_protein = number
+ max_domain_copy_number_per_protein = passing_domains_per_protein
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)"
+ else # no pass
+ log << domain_fail_counter.to_s + ": " + sequence.to_s + " fails 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
+ domain_fail_counter += 1
end
if number > out_of
- error_msg = "number > out_of ! (this should not have happened)"
+ 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 )
+ 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 )
error_msg = "this should not have happened"
raise StandardError, error_msg
end
- else
+ else # no pass
if failed_seqs.find_by_name_start( sequence, true ).length < 1
add_sequence( sequence, in_msa, failed_seqs )
proteins_with_failing_domains += 1
end
hmmscan_datas.clear
end
+
+ end # results.each do | r |
+
+ if (prev_query != nil) && (!saw_target)
+ log << domain_not_present_counter.to_s + ": " + prev_query.to_s + " lacks target domain" + ld
+ domain_not_present_counter += 1
end
if domain_pass_counter < 1
raise IOError, error_msg
end
+ if ( domain_not_present_counter + passed_seqs.get_number_of_seqs + proteins_with_failing_domains ) != protein_counter
+ error_msg = "not present + passing + not passing != proteins in sequence (fasta) file (this should not have happened)"
+ raise StandardError, error_msg
+ end
+
+ puts
+ log << ld
+
+ log << ld
+ avg_pass = ( passing_target_length_sum / domain_pass_counter )
+ puts( "Passing target domain lengths: average: " + avg_pass.to_s )
+ log << "Passing target domain lengths: average: " + avg_pass.to_s
+ log << ld
+ puts( "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + " - " + passing_target_length_max.to_s)
+ log << "Passing target domain lengths: min-max: " + passing_target_length_min.to_s + " - " + passing_target_length_max.to_s
+ log << ld
+ puts( "Passing target domain iE: min-max: " + passing_target_ie_min.to_s + " - " + passing_target_ie_max.to_s)
+ log << "Passing target domain iE: min-max: " + passing_target_ie_min.to_s + " - " + passing_target_ie_max.to_s
+ log << ld
+ puts( "Passing target domains: sum: " + domain_pass_counter.to_s )
+ log << "Passing target domains: sum: " + domain_pass_counter.to_s
+ log << ld
+ log << ld
+ puts
+ sum = domain_pass_counter + domain_fail_counter
+ avg_all = overall_target_length_sum / sum
+ puts( "All target domain lengths: average: " + avg_all.to_s )
+ log << "All target domain lengths: average: " + avg_all.to_s
+ log << ld
+ puts( "All target domain lengths: min-max: " + overall_target_length_min.to_s + " - " + overall_target_length_max.to_s)
+ log << "All target domain lengths: min-max: " + overall_target_length_min.to_s + " - " + overall_target_length_max.to_s
+ log << ld
+ puts( "All target target domain iE: min-max: " + overall_target_ie_min.to_s + " - " + overall_target_ie_max.to_s)
+ log << "All target target domain iE: min-max: " + overall_target_ie_min.to_s + " - " + overall_target_ie_max.to_s
+ log << ld
+ puts( "All target domains: sum: " + sum.to_s )
+ log << "All target domains: sum: " + sum.to_s
+
+ puts
+ puts( "Proteins with passing target domain(s): " + passed_seqs.get_number_of_seqs.to_s )
+ puts( "Proteins with no passing target domain: " + proteins_with_failing_domains.to_s )
+ puts( "Proteins with no target domain : " + domain_not_present_counter.to_s )
+
+ log << ld
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
+ puts
+ puts( "Max target domain copy number per protein: " + max_domain_copy_number_per_protein.to_s )
+ log << "Max target domain copy number per protein: " + max_domain_copy_number_per_protein.to_s
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
+ puts( "First target protein with this copy number: " + max_domain_copy_number_sequence )
+ log << "First target protein with this copy number: " + max_domain_copy_number_sequence
log << ld
end
write_msa( failed_seqs, failed_seqs_outfile )
if out_msa_pairs
- write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta")
+ write_msa( out_msa_pairs, outfile + "_" + min_linker.to_s + ".fasta")
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
end
if out_msa_single_domains_protein_seqs
- write_msa( out_msa_single_domains_protein_seqs, outfile +"_proteins_with_singles.fasta" )
+ write_msa( out_msa_single_domains_protein_seqs, outfile + "_proteins_with_singles.fasta" )
end
if out_msa_close_pairs_protein_seqs
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
+ 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
- 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
+ log << "passing target domains : " + domain_pass_counter.to_s + ld
+ log << "failing target domains : " + domain_fail_counter.to_s + ld
+ log << "proteins in sequence (fasta) file : " + in_msa.get_number_of_seqs.to_s + ld
+ log << "proteins in hmmscan outputfile : " + protein_counter.to_s + ld
+ log << "proteins with passing target domain(s) : " + passed_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with no passing target domain : " + proteins_with_failing_domains.to_s + ld
+ log << "proteins with no target domain : " + domain_not_present_counter.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
+ 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 with single domains : " + out_msa_single_domains_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with close pair domains : " + out_msa_close_pairs_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with close pair domains only : " + out_msa_close_pairs_only_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with isolated domains : " + out_msa_isolated_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with isolated domains only : " + out_msa_isolated_only_protein_seqs.get_number_of_seqs.to_s + ld
+ log << "proteins with close pair and isolated domains: " + out_msa_isolated_and_close_pair_protein_seqs.get_number_of_seqs.to_s + ld
end
log << ld
end # parse
-
private
def write_msa( msa, filename )
end
end
-
def add_sequence( sequence_name, in_msa, add_to_msa )
seqs = in_msa.find_by_name_start( sequence_name, true )
if ( seqs.length < 1 )
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,
- 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 )
+ 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
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 )
+ 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 )
+ 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
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 ) ) )
+ ( 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 )
+ 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
from = 1
end
to = to + ADD_TO_CLOSE_PAIRS
- if to > in_msa.get_length
- to = in_msa.get_length
+ temp_seqs = in_msa.find_by_name_start( seq_name, true )
+ temp_seq = in_msa.get_sequence( temp_seqs[ 0 ] )
+ if to > temp_seq.get_length
+ to = temp_seq.get_length
end
end
extract_domain( seq_name,
- index.to_s + "+" + ( index + 1 ).to_s,
- actual_out_of,
- from,
- hmmscan_data.env_to,
- in_msa,
- out_msa_pairs,
- add_position,
- add_domain_number,
- add_species )
+ index.to_s + "+" + ( index + 1 ).to_s,
+ actual_out_of,
+ from,
+ to,
+ in_msa,
+ out_msa_pairs,
+ add_position,
+ add_domain_number,
+ add_species )
saw_close_pair = true
end
end
end # def process_hmmscan_data
def extract_domain( sequence,
- number,
- out_of,
- seq_from,
- seq_to,
- in_msa,
- out_msa,
- add_position,
- add_domain_number,
- add_species )
+ number,
+ out_of,
+ seq_from,
+ seq_to,
+ in_msa,
+ out_msa,
+ add_position,
+ add_domain_number,
+ add_species )
if number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
error_msg = "number=" + number.to_s + ", out of=" + out_of.to_s
raise StandardError, error_msg
error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
raise IOError, error_msg
end
- # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
+ # hmmscan is 1 based, whereas 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
git://source.jalview.org / jalview.git / blobdiff