def run
- Util.print_program_information( PRG_NAME,
- PRG_VERSION,
- PRG_DESC,
- PRG_DATE,
- COPYRIGHT,
- CONTACT,
- WWW,
- STDOUT )
+ # Util.print_program_information( PRG_NAME,
+ # PRG_VERSION,
+ # PRG_DESC,
+ # PRG_DATE,
+ # COPYRIGHT,
+ # CONTACT,
+ # WWW,
+ # STDOUT )
begin
cla = CommandLineArguments.new( ARGV )
parse_descriptions = true
end
- puts()
- puts( "hmmpfam outputfile : " + inpath )
- puts( "outputfile : " + outpath )
- puts( "species : " + species )
- if ( i_e_value_threshold >= 0.0 )
- puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
- else
- puts( "i-E-value threshold : no threshold" )
- end
- if ( parse_descriptions )
- puts( "parse descriptions : true" )
- else
- puts( "parse descriptions : false" )
- end
- if ( ignore_dufs )
- puts( "ignore DUFs : true" )
- else
- puts( "ignore DUFs : false" )
- end
- if ( column_delimiter == "\t" )
- puts( "column delimiter : TAB" )
- else
- puts( "column delimiter : " + column_delimiter )
- end
- if fs_e_value_threshold >= 0.0
- puts( "E-value threshold : " + fs_e_value_threshold.to_s )
- else
- puts( "E-value threshold : no threshold" )
- end
- if !hmm_for_protein_output.empty?
- puts( "HMM for proteins : " + hmm_for_protein_output )
- end
- if !uniprot.empty?
- puts( "Uniprot : " + uniprot )
- end
- puts()
+# puts()
+# puts( "hmmpfam outputfile : " + inpath )
+# puts( "outputfile : " + outpath )
+# puts( "species : " + species )
+# if ( i_e_value_threshold >= 0.0 )
+# puts( "i-E-value threshold : " + i_e_value_threshold.to_s )
+# else
+# puts( "i-E-value threshold : no threshold" )
+# end
+# if ( parse_descriptions )
+# puts( "parse descriptions : true" )
+# else
+# puts( "parse descriptions : false" )
+# end
+# if ( ignore_dufs )
+# puts( "ignore DUFs : true" )
+# else
+# puts( "ignore DUFs : false" )
+# end
+# if ( column_delimiter == "\t" )
+# puts( "column delimiter : TAB" )
+# else
+# puts( "column delimiter : " + column_delimiter )
+# end
+# if fs_e_value_threshold >= 0.0
+# puts( "E-value threshold : " + fs_e_value_threshold.to_s )
+# else
+# puts( "E-value threshold : no threshold" )
+# end
+# if !hmm_for_protein_output.empty?
+# puts( "HMM for proteins : " + hmm_for_protein_output )
+# end
+# if !uniprot.empty?
+# puts( "Uniprot : " + uniprot )
+# end
+# puts()
begin
parse( inpath,
end
domain_counts = get_domain_counts()
- puts
- puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
- puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
- puts
- puts( Util.draw_histogram( domain_counts, "#" ) )
- puts
- Util.print_message( PRG_NAME, 'OK' )
- puts
+# puts
+# puts( "domain counts (considering potential i-E-value threshold and ignoring of DUFs):" )
+# puts( "(number of different domains: " + domain_counts.length.to_s + ")" )
+# puts
+# puts( Util.draw_histogram( domain_counts, "#" ) )
+# puts
+# Util.print_message( PRG_NAME, 'OK' )
+# puts
end # def run
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- false,
+ uniprot,
species )
end
hmmscan_results_per_protein.clear
if r.model == hmm_for_protein_output
- if i_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold
+ if fs_e_value_threshold > 0.0 && r.fs_e_value > fs_e_value_threshold
return
end
end