require 'lib/evo/util/util'
require 'lib/evo/util/command_line_arguments'
require 'lib/evo/io/parser/hmmscan_parser'
-require 'lib/evo/io/web/uniprotkb'
module Evoruby
class HmmscanSummary
PRG_NAME = "hsp"
- PRG_VERSION = "2.001"
+ PRG_VERSION = "2.002"
PRG_DESC = "hmmscan summary"
- PRG_DATE = "2013.10.23"
+ PRG_DATE = "130319"
COPYRIGHT = "2013 Christian M Zmasek"
CONTACT = "phyloxml@gmail.com"
WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
HMM_FOR_PROTEIN_OUTPUT = "m"
IGNORE_DUF_OPTION = "i"
PARSE_OUT_DESCRIPITION_OPTION = "a"
- UNIPROT = "u"
HELP_OPTION_1 = "help"
HELP_OPTION_2 = "h"
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 )
allowed_opts.push( IGNORE_DUF_OPTION )
allowed_opts.push( PARSE_OUT_DESCRIPITION_OPTION )
allowed_opts.push( HMM_FOR_PROTEIN_OUTPUT )
- allowed_opts.push( UNIPROT )
allowed_opts.push( SPECIES_OPTION )
disallowed = cla.validate_allowed_options_as_str( allowed_opts )
end
end
-
-
fs_e_value_threshold = -1.0
if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
begin
end
end
- uniprot = ""
- if ( cla.is_option_set?( UNIPROT ) )
- begin
- uniprot = cla.get_option_value( UNIPROT )
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
- end
- end
-
species = "HUMAN"
if ( cla.is_option_set?( SPECIES_OPTION ) )
begin
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
+ puts()
begin
parse( inpath,
parse_descriptions,
fs_e_value_threshold,
hmm_for_protein_output,
- uniprot,
species )
rescue IOError => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
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
get_descriptions,
fs_e_value_threshold,
hmm_for_protein_output,
- uniprot,
species )
Util.check_file_for_readability( inpath )
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- uniprot,
species )
end
hmmscan_results_per_protein.clear
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- uniprot,
species )
end
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- uniprotkb,
species )
dc = 0
end
s << "\t"
- if !uniprotkb.empty?
- #e = UniprotKB::get_entry_by_id( process_id( own.query ) )
-
- #if e != nil
- # s << uniprot_annotation( e )
- # # s << "\uniprot_annotationt"
- #end
- end
-
overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
s << overview + "\t"
prev_r = nil
hmmscan_results_per_protein_filtered.each do | r |
-
if prev_r != nil
s << make_interdomain_sequence( r.env_from - prev_r.env_to - 1 )
else
s << "]"
prev_r = r
end
- s << make_interdomain_sequence( own.qlen - prev_r.env_from, false )
+ s << make_interdomain_sequence( own.qlen - prev_r.env_to, false )
puts s
end
- def uniprot_annotation( e )
- s = ""
- pdb_ids = e.get_pdb_ids
- if !pdb_ids.empty?
- pdb_ids.each do | pdb |
- s << pdb << ", "
- end
- else
- s << "-"
- end
- s
- end
-
def calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
linkers = ""
prev_r = nil
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