From b8e92404ed8c15340596fdae0474272cd29eaed4 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Sat, 29 Sep 2012 05:09:38 +0000 Subject: [PATCH] in progress --- .../evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb index 99c6ec5..8c66f42 100644 --- a/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/io/parser/hmmscan_domain_extractor.rb @@ -61,7 +61,7 @@ module Evoruby failed_seqs = Msa.new passed_seqs = Msa.new out_msa_pairs = nil - out_msa_distance_partners = nil + out_msa_distant_partners = nil out_msa_singlets = nil if min_linker out_msa_pairs = Msa.new @@ -78,7 +78,7 @@ module Evoruby max_domain_copy_number_per_protein = -1 max_domain_copy_number_sequence = "" - prev_sequence = "" + prev_sequence = nil prev_number = nil prev_env_from = nil prev_env_to = nil @@ -135,13 +135,13 @@ module Evoruby if ( ( e_value_threshold < 0.0 ) || ( prev_i_e_value <= e_value_threshold ) ) && ( ( length_threshold <= 0 ) || ( ( prev_env_to - prev_env_from + 1 ) >= length_threshold.to_f ) ) - if sequence != prev_sequence + if prev_sequence && sequence != prev_sequence prev_is_pair = false end if out_of == 1 - if sequence == prev_sequence + if rev_sequence && sequence == prev_sequence puts "sequence == prev_sequence && out_of == 1" exit end @@ -159,7 +159,7 @@ module Evoruby trim_name , add_species ) - elsif sequence == prev_sequence + elsif prev_sequence && sequence == prev_sequence if ( env_from - prev_env_to ) <= min_linker ####### extract_domain( sequence, @@ -273,7 +273,7 @@ module Evoruby end if out_msa_distant_partners - write_msa( out_msa_distant_partners, outfile +"_singles" ) + write_msa( out_msa_distant_partners, outfile +"_dist" ) end -- 1.7.10.2