#
# $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $
#
-# last modified: 121003
require 'set'
require 'lib/evo/util/util'
require 'lib/evo/util/command_line_arguments'
require 'lib/evo/io/parser/hmmscan_parser'
-require 'lib/evo/io/parser/uniprot_parser'
require 'lib/evo/io/web/uniprotkb'
module Evoruby
class HmmscanSummary
PRG_NAME = "hsp"
- PRG_VERSION = "2.000"
+ PRG_VERSION = "2.001"
PRG_DESC = "hmmscan summary"
- PRG_DATE = "2012.10.23"
- COPYRIGHT = "2012 Christian M Zmasek"
- CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
+ PRG_DATE = "2013.10.23"
+ COPYRIGHT = "2013 Christian M Zmasek"
+ CONTACT = "phyloxml@gmail.com"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
DELIMITER_OPTION = "d"
+ SPECIES_OPTION = "s"
I_E_VALUE_THRESHOLD_OPTION = "ie"
FS_E_VALUE_THRESHOLD_OPTION = "pe"
HMM_FOR_PROTEIN_OUTPUT = "m"
def run
- ukb = UniprotKB.new
- ukb.get
-
- 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( 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 )
if ( disallowed.length > 0 )
end
end
+
+
fs_e_value_threshold = -1.0
if ( cla.is_option_set?( FS_E_VALUE_THRESHOLD_OPTION ) )
begin
end
end
+ species = "HUMAN"
+ if ( cla.is_option_set?( SPECIES_OPTION ) )
+ begin
+ species = cla.get_option_value( SPECIES_OPTION )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )
+ end
+ end
+
ignore_dufs = false
if ( cla.is_option_set?( IGNORE_DUF_OPTION ) )
ignore_dufs = true
parse_descriptions = true
end
- puts()
- puts( "hmmpfam outputfile : " + inpath )
- puts( "outputfile : " + outpath )
- 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,
parse_descriptions,
fs_e_value_threshold,
hmm_for_protein_output,
- uniprot )
+ 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 )
-
-
+ uniprot,
+ species )
Util.check_file_for_readability( inpath )
Util.check_file_for_writability( outpath )
hmmscan_parser = HmmscanParser.new( inpath )
results = hmmscan_parser.parse
- uniprot_entries = nil
- if !uniprot.empty? && !hmm_for_protein_output.empty?
- uniprot_entries = read_uniprot( results, uniprot )
- end
-
outfile = File.open( outpath, "a" )
query = ""
hmmscan_results_per_protein = []
-
-
prev_query = ""
results.each do | r |
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- uniprot_entries )
+ uniprot,
+ species )
end
hmmscan_results_per_protein.clear
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,
- uniprot_entries )
+ uniprot,
+ species )
end
outfile.flush()
outfile.close()
-
end # def parse
def process_id( id )
id
end
- def read_uniprot( hmmscan_results, uniprot )
- ids = Set.new
- hmmscan_results.each do | r |
-
- ids << process_id( r.query )
- end
- uniprot_parser = UniprotParser.new uniprot
- uniprot_entries = uniprot_parser.parse ids
- uniprot_entries
- end
-
def count_model( model )
if ( @domain_counts.has_key?( model ) )
count = @domain_counts[ model ].to_i
fs_e_value_threshold,
hmm_for_protein_output,
i_e_value_threshold,
- uniprot_entries )
+ uniprotkb,
+ species )
dc = 0
# filter according to i-Evalue threshold
hmmscan_results_per_protein_filtered = []
hmmscan_results_per_protein.each do | r |
+
+
if r.model == hmm_for_protein_output
- if 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
- 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
s = ""
s << own.query + "\t"
- s << "HUMAN" + "\t"
+ s << species + "\t"
s << own.fs_e_value.to_s + "\t"
s << own.qlen.to_s + "\t"
s << dc.to_s + "\t"
s << r.model + " "
end
s << "\t"
- e = uniprot_entries[ process_id( own.query ) ]
- if e != nil && e.de != nil
- e.de.each { |i| s << i + " " }
- else
- s << "-"
- end
- s << "\t"
-
- if e != nil && e.gn != nil
- e.gn.each { |i| s << i + " " }
- else
- s << "-"
- end
+ 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
- s << "\t"
overview = make_overview( hmmscan_results_per_protein_filtered, hmm_for_protein_output )
- s << overview + "\t"
+ s << overview + "\t"
s << calc_linkers( hmmscan_results_per_protein_filtered, hmm_for_protein_output ) + "\t"
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 = ""
end
-
def print_help()
puts( "Usage:" )
puts()
puts( " -" + IGNORE_DUF_OPTION + ": ignore DUFs" )
puts( " -" + FS_E_VALUE_THRESHOLD_OPTION + ": E-value threshold for full protein sequences, only for protein summary" )
puts( " -" + HMM_FOR_PROTEIN_OUTPUT + ": HMM for protein summary" )
+ puts( " -" + SPECIES_OPTION + ": species for protein summary" )
puts()
end
git://source.jalview.org / jalview.git / blobdiff