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[jalview.git]
/
forester
/
ruby
/
evoruby
/
lib
/
evo
/
tool
/
hmmscan_summary.rb
diff --git
a/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
b/forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
index
913be50
..
55ba7a4
100644
(file)
--- a/
forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
+++ b/
forester/ruby/evoruby/lib/evo/tool/hmmscan_summary.rb
@@
-67,7
+67,7
@@
module Evoruby
end
if ( cla.is_option_set?( HELP_OPTION_1 ) ||
end
if ( cla.is_option_set?( HELP_OPTION_1 ) ||
- cla.is_option_set?( HELP_OPTION_2 ) )
+ cla.is_option_set?( HELP_OPTION_2 ) )
print_help
exit( 0 )
end
print_help
exit( 0 )
end
@@
-118,7
+118,7
@@
module Evoruby
end
end
end
end
-
+
fs_e_value_threshold = -1.0
if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
fs_e_value_threshold = -1.0
if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
@@
-151,7
+151,7
@@
module Evoruby
end
species = "HUMAN"
end
species = "HUMAN"
- if ( cla.is_option_set?( SPECIES_OPTION ) )
+ if ( cla.is_option_set?( SPECIES_OPTION ) )
begin
species = cla.get_option_value( SPECIES_OPTION )
rescue ArgumentError => e
begin
species = cla.get_option_value( SPECIES_OPTION )
rescue ArgumentError => e
@@
-279,21
+279,21
@@
module Evoruby
env_to = r.env_to
if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) &&
env_to = r.env_to
if ( ( i_e_value_threshold < 0.0 ) || ( i_e_value <= i_e_value_threshold ) ) &&
- ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
+ ( !ignore_dufs || ( model !~ /^DUF\d+/ ) )
count_model( model )
outfile.print( query +
count_model( model )
outfile.print( query +
- column_delimiter )
+ column_delimiter )
if ( get_descriptions )
outfile.print( desc +
if ( get_descriptions )
outfile.print( desc +
- column_delimiter )
+ column_delimiter )
end
outfile.print( model +
end
outfile.print( model +
- column_delimiter +
- env_from.to_s +
- column_delimiter +
- env_to.to_s +
- column_delimiter +
- i_e_value.to_s )
+ column_delimiter +
+ env_from.to_s +
+ column_delimiter +
+ env_to.to_s +
+ column_delimiter +
+ i_e_value.to_s )
outfile.print( Constants::LINE_DELIMITER )
end
outfile.print( Constants::LINE_DELIMITER )
end
@@
-304,7
+304,8
@@
module Evoruby
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- true )
+ false,
+ species )
end
hmmscan_results_per_protein.clear
end
end
hmmscan_results_per_protein.clear
end
@@
-319,12
+320,14
@@
module Evoruby
end
end
end
end
end
end
+
if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
process_hmmscan_results_per_protein( hmmscan_results_per_protein,
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
if !hmm_for_protein_output.empty? && !hmmscan_results_per_protein.empty?
process_hmmscan_results_per_protein( hmmscan_results_per_protein,
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- true )
+ false,
+ species )
end
outfile.flush()
end
outfile.flush()
@@
-355,7
+358,8
@@
module Evoruby
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- uniprotkb )
+ uniprotkb,
+ species )
dc = 0
# filter according to i-Evalue threshold
dc = 0
# filter according to i-Evalue threshold
@@
-363,12
+367,15
@@
module Evoruby
hmmscan_results_per_protein_filtered = []
hmmscan_results_per_protein.each do | r |
hmmscan_results_per_protein_filtered = []
hmmscan_results_per_protein.each do | r |
+
+
+
if r.model == hmm_for_protein_output
if r.model == hmm_for_protein_output
- if r.fs_e_value > fs_e_value_threshold
+ if i_e_value_threshold >= 0.0 && r.fs_e_value > fs_e_value_threshold
return
end
end
return
end
end
- if r.i_e_value <= i_e_value_threshold
+ if i_e_value_threshold < 0 || r.i_e_value <= i_e_value_threshold
hmmscan_results_per_protein_filtered << r
if r.model == hmm_for_protein_output
dc += 1
hmmscan_results_per_protein_filtered << r
if r.model == hmm_for_protein_output
dc += 1
@@
-401,12
+408,13
@@
module Evoruby
s << r.model + " "
end
s << "\t"
s << r.model + " "
end
s << "\t"
- e = UniprotKB::get_entry_by_id( process_id( own.query ) )
- if e != nil
- s << uniprot_annotation( e )
- s << "\uniprot_annotationt"
- end
+ #e = UniprotKB::get_entry_by_id( process_id( own.query ) )
+
+ #if e != nil
+ # s << uniprot_annotation( e )
+ # # s << "\uniprot_annotationt"
+ #end
overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )