#
# = lib/evo/tool/hmmscan_summary.rb - HmmscanSummary class
#
-# Copyright:: Copyright (C) 2012 Christian M. Zmasek
-# License:: GNU Lesser General Public License (LGPL)
-#
-# $Id: hmmscan_parser.rb,v 1.5 2010/12/13 19:00:11 cmzmasek Exp $
-#
-# last modified: 121003
+# Copyright:: Copyright (C) 2017 Christian M Zmasek
+# License:: GNU Lesser General Public License (LGPL)
require 'set'
-
require 'lib/evo/util/constants'
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 = "2.000"
- PRG_DESC = "hmmscan summary"
- PRG_DATE = "2012.10.23"
- COPYRIGHT = "2012 Christian M Zmasek"
- CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
+ PRG_VERSION = "2.003"
+ PRG_DESC = "Summarize hmmscan output tables into simpler tables"
+ PRG_DATE = "170213"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
DELIMITER_OPTION = "d"
SPECIES_OPTION = "s"
HMM_FOR_PROTEIN_OUTPUT = "m"
IGNORE_DUF_OPTION = "i"
PARSE_OUT_DESCRIPITION_OPTION = "a"
- UNIPROT = "u"
HELP_OPTION_1 = "help"
HELP_OPTION_2 = "h"
- USE_AVOID_HMMS = true
- AVOID_HHMS = [ "RRM_1", "RRM_2", "RRM_3", "RRM_4", "RRM_5", "RRM_6" ]
- LIMIT_FOR_CLOSE_DOMAINS = 20
+ USE_AVOID_HMMS = false
+ AVOID_HHMS = [ "x", "y", "z" ]
+ LIMIT_FOR_CLOSE_DOMAINS = 20 # Used for protein architecture summary
def initialize
@domain_counts = Hash.new
def run
-
-
Util.print_program_information( PRG_NAME,
- PRG_VERSION,
- PRG_DESC,
- PRG_DATE,
- COPYRIGHT,
- CONTACT,
- WWW,
- STDOUT )
+ PRG_VERSION,
+ PRG_DESC,
+ PRG_DATE,
+ WWW,
+ STDOUT )
+
+ if ( ARGV == nil || ( ARGV.length < 1 ) )
+ print_help
+ exit( -1 )
+ end
begin
cla = CommandLineArguments.new( ARGV )
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
- if ( cla.get_number_of_files != 2 )
- print_help
- exit( -1 )
- end
-
allowed_opts = Array.new
allowed_opts.push( DELIMITER_OPTION )
allowed_opts.push( I_E_VALUE_THRESHOLD_OPTION )
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 )
if ( disallowed.length > 0 )
Util.fatal_error( PRG_NAME,
- "unknown option(s): " + disallowed,
- STDOUT )
+ "unknown option(s): " + disallowed,
+ STDOUT )
end
inpath = cla.get_file_name( 0 )
- outpath = cla.get_file_name( 1 )
+
+ outpath = ""
+ if ( cla.get_number_of_files == 1 )
+ outpath = inpath + Constants::DOMAIN_TABLE_SUFFIX
+ elsif ( cla.get_number_of_files == 2 )
+ outpath = cla.get_file_name( 1 )
+ else
+ print_help
+ exit( -1 )
+ end
column_delimiter = "\t"
if ( cla.is_option_set?( DELIMITER_OPTION ) )
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 ) )
+ if ( cla.is_option_set?( SPECIES_OPTION ) )
begin
species = cla.get_option_value( SPECIES_OPTION )
rescue ArgumentError => e
end
puts()
- puts( "hmmpfam outputfile : " + inpath )
+ puts( "hmmscan 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
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" )
+ puts( "column delimiter : " + column_delimiter )
end
if !hmm_for_protein_output.empty?
puts( "HMM for proteins : " + hmm_for_protein_output )
- end
- if !uniprot.empty?
- puts( "Uniprot : " + uniprot )
+ puts( "species : " + species )
+ 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
end
puts()
begin
parse( inpath,
- outpath,
- column_delimiter,
- i_e_value_threshold,
- ignore_dufs,
- parse_descriptions,
- fs_e_value_threshold,
- hmm_for_protein_output,
- uniprot,
- species )
+ outpath,
+ column_delimiter,
+ i_e_value_threshold,
+ ignore_dufs,
+ parse_descriptions,
+ fs_e_value_threshold,
+ hmm_for_protein_output,
+ 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, "wrote: " + outpath )
+ Util.print_message( PRG_NAME, "next step in standard analysis pipeline: d2f.rb")
Util.print_message( PRG_NAME, 'OK' )
puts
# raises ArgumentError, IOError
def parse( inpath,
- outpath,
- column_delimiter,
- i_e_value_threshold,
- ignore_dufs,
- get_descriptions,
- fs_e_value_threshold,
- hmm_for_protein_output,
- uniprot,
- species )
-
-
+ outpath,
+ column_delimiter,
+ i_e_value_threshold,
+ ignore_dufs,
+ get_descriptions,
+ fs_e_value_threshold,
+ hmm_for_protein_output,
+ species )
Util.check_file_for_readability( inpath )
Util.check_file_for_writability( outpath )
hmmscan_results_per_protein = []
-
-
prev_query = ""
results.each do | r |
model = r.model
+ desc = r.desc
query = r.query
i_e_value = r.i_e_value
env_from = r.env_from
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 +
- column_delimiter )
+ column_delimiter )
if ( get_descriptions )
outfile.print( desc +
- column_delimiter )
+ column_delimiter )
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
if !prev_query.empty? && prev_query != query
if !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,
- false,
- species )
+ fs_e_value_threshold,
+ hmm_for_protein_output,
+ i_e_value_threshold,
+ species )
end
hmmscan_results_per_protein.clear
end
end
end
end
- puts hmm_for_protein_output
- puts hmmscan_results_per_protein
+
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,
- false,
- species )
+ fs_e_value_threshold,
+ hmm_for_protein_output,
+ i_e_value_threshold,
+ species )
end
outfile.flush()
outfile.close()
-
end # def parse
def process_id( id )
id
end
-
-
def count_model( model )
if ( @domain_counts.has_key?( model ) )
count = @domain_counts[ model ].to_i
end
def process_hmmscan_results_per_protein( hmmscan_results_per_protein,
- fs_e_value_threshold,
- hmm_for_protein_output,
- i_e_value_threshold,
- uniprotkb,
- species )
-
- puts "+"
+ fs_e_value_threshold,
+ hmm_for_protein_output,
+ i_e_value_threshold,
+ 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 << r.model + " "
end
s << "\t"
- puts s
- #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 )
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
s
end
-
-
def print_help()
puts( "Usage:" )
puts()
- puts( " " + PRG_NAME + ".rb [options] <hmmscan outputfile> <outputfile>" )
+ puts( " " + PRG_NAME + ".rb [options] <hmmscan outputfile> [outputfile]" )
+ puts()
+ puts( " options: -" + DELIMITER_OPTION + "=<s> : column delimiter for outputfile, default is TAB" )
+ puts( " -" + I_E_VALUE_THRESHOLD_OPTION + "=<f>: i-E-value threshold, default is no threshold" )
+ puts( " -" + PARSE_OUT_DESCRIPITION_OPTION + " : parse query description (in addition to query name)" )
+ puts( " -" + IGNORE_DUF_OPTION + " : ignore DUFs" )
+ puts( " -" + HMM_FOR_PROTEIN_OUTPUT + "=<s> : HMM for protein architectures summary" )
+ puts( " -" + FS_E_VALUE_THRESHOLD_OPTION + "=<f>: E-value threshold for full protein sequences, only for protein architectures summary" )
+ puts( " -" + SPECIES_OPTION + "=<s> : species for protein architectures summary" )
+ puts()
+ puts( " [next step in standard analysis pipeline: d2f.rb]")
+ puts()
+ puts( "Examples:" )
+ puts()
+ puts( " " + "hmmscan --max --domtblout P53_hmmscan_#{Constants::PFAM_V_FOR_EX}_10 -E 10 Pfam-A.hmm P53_ni.fasta" )
puts()
- puts( " options: -" + DELIMITER_OPTION + ": column delimiter for outputfile, default is TAB" )
- puts( " -" + I_E_VALUE_THRESHOLD_OPTION + ": i-E-value threshold, default is no threshold" )
- puts( " -" + PARSE_OUT_DESCRIPITION_OPTION + ": parse query description (in addition to query name)" )
- 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( " " + PRG_NAME + ".rb P53_hmmscan_300_10" )
puts()
end
git://source.jalview.org / jalview.git / blobdiff