#
# = lib/evo/apps/multi_sequence_extractor.rb - MultiSequenceExtractor class
#
-# Copyright:: Copyright (C) 2006-2008 Christian M. Zmasek
+# Copyright:: Copyright (C) 2014 Christian M. Zmasek
# License:: GNU Lesser General Public License (LGPL)
#
-# $Id: multi_sequence_extractor.rb,v 1.10 2010/12/13 19:00:11 cmzmasek Exp $
require 'lib/evo/util/constants'
require 'lib/evo/io/writer/fasta_writer'
require 'lib/evo/util/command_line_arguments'
-
-
module Evoruby
class MultiSequenceExtractor
PRG_NAME = "mse"
- PRG_VERSION = "1.02"
+ PRG_VERSION = "1.04"
PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files"
- PRG_DATE = "2012.07.20"
- COPYRIGHT = "2008-2012 Christian M Zmasek"
- CONTACT = "phylosoft@gmail.com"
- WWW = "www.phylosoft.org"
+ PRG_DATE = "140318"
+ COPYRIGHT = "2014 Christian M Zmasek"
+ CONTACT = "phyloxml@gmail.com"
+ WWW = "https://sites.google.com/site/cmzmasek/home/software/forester"
HELP_OPTION_1 = 'help'
HELP_OPTION_2 = 'h'
NORMALIZED_IDS_MAP_SUFFIX = ".nim"
PROTEINS_LIST_FILE_SEPARATOR = "\t"
+ def initialize()
+ @file_to_msa = Hash.new
+ @seqs = 0
+ end
def run()
exit( 0 )
end
- if ( cla.get_number_of_files != 4 && cla.get_number_of_files != 5 )
+ if ( cla.get_number_of_files != 5 )
print_help
exit( -1 )
end
input_dir = cla.get_file_name( 1 )
out_dir = cla.get_file_name( 2 )
out_dir_doms = cla.get_file_name( 3 )
- mapping_file = nil
+ mapping_file = cla.get_file_name( 4 )
- if ( cla.get_number_of_files == 5 )
- mapping_file = cla.get_file_name( 4 )
- begin
- Util.check_file_for_readability( mapping_file )
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
- end
+ begin
+ Util.check_file_for_readability( mapping_file )
+ rescue ArgumentError => e
+ Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
extension = 0
extract_linkers = true
end
- if !File.exist?( input_dir )
+ unless File.exist?( out_dir )
+ Dir.mkdir( out_dir )
+ end
+ unless File.exist?( out_dir_doms )
+ Dir.mkdir( out_dir_doms )
+ end
+
+ unless File.exist?( input_dir )
Util.fatal_error( PRG_NAME, "error: input directory [#{input_dir}] does not exist" )
end
- if !File.exist?( out_dir )
+ unless File.exist?( out_dir )
Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir}] does not exist" )
end
- if !File.exist?( out_dir_doms )
+ unless File.exist?( out_dir_doms )
Util.fatal_error( PRG_NAME, "error: output directory [#{out_dir_doms}] does not exist" )
end
- if !File.directory?( input_dir )
+ unless File.directory?( input_dir )
Util.fatal_error( PRG_NAME, "error: [#{input_dir}] is not a directory" )
end
- if !File.directory?( out_dir )
+ unless File.directory?( out_dir )
Util.fatal_error( PRG_NAME, "error: [#{out_dir}] is not a directory" )
end
- if !File.directory?( out_dir_doms )
+ unless File.directory?( out_dir_doms )
Util.fatal_error( PRG_NAME, "error: [#{out_dir_doms}] is not a directory" )
end
-
log = String.new
log << "Program : " + PRG_NAME + ld
log << "Output dir : " + out_dir + ld
puts( "Output dir domains : " + out_dir_doms )
log << "Output dir domains : " + out_dir_doms + ld
- if ( mapping_file != nil )
- puts( "Mapping file : " + mapping_file )
- log << "Mapping file : " + mapping_file + ld
- end
+ puts( "Mapping file : " + mapping_file )
+ log << "Mapping file : " + mapping_file + ld
if extension > 0
puts( "Extension : " + extension.to_s )
log << "Extension : " + extension.to_s + ld
log << "Date : " + Time.now.to_s + ld
puts
- if ( mapping_file != nil )
- species_codes_to_paths = extract_mappings( mapping_file )
- end
+ species_codes_to_paths = extract_mappings( mapping_file )
input_files = obtain_inputfiles( input_dir, seq_names_files_suffix )
puts basename
File.open( input_file ) do | file |
+ species_counter = 1
while line = file.gets
line.strip!
if !Util.is_string_empty?( line ) && !(line =~ /\s*#/ )
Util.fatal_error( PRG_NAME, "unexpected format: " + line )
end
species = values[ 0 ]
- if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
- next
- end
+ #if species == "BRADI" || species == "ASPNG" || species == "SCLSC" || species == "PTEVA" || species == "EIMTE"
+ # next
+ #end
seq_name = values[ 1 ]
domain_ranges = nil
if ( values.length > 3 )
print_counts( per_species_counter, log, Constants::LINE_DELIMITER )
per_species_counter = 0
end
- puts " " + current_species + " [" + my_readlink + "]"
- log << current_species + " [" + my_readlink + "]" + Constants::LINE_DELIMITER
+ puts " " + species_counter.to_s + ":" + current_species + " [" + my_readlink + "]"
+ log << species_counter.to_s << ": " << current_species << " [" + my_readlink + "]" << Constants::LINE_DELIMITER
+ species_counter += 1
end
- puts " " + seq_name
- log << " " + seq_name + Constants::LINE_DELIMITER
+ log << " " << seq_name << Constants::LINE_DELIMITER
per_species_counter = per_species_counter + 1
seq = nil
- if current_msa.find_by_name_start( seq_name, true ).size > 0
- begin
- seq = current_msa.get_by_name_start( seq_name, true ).copy
- rescue ArgumentError => e
- Util.fatal_error( PRG_NAME, "error: " + e.to_s )
- end
- else
+ indices = current_msa.find_by_name_start( seq_name, true )
+ if indices.size == 1
+ seq = current_msa.get_sequence( indices[ 0 ] )
+ elsif indices.size == 0
# Not found, try finding by partial match.
begin
seq = current_msa.get_by_name( seq_name, true, true )
rescue ArgumentError => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
+ else
+ Util.fatal_error( PRG_NAME, "error: seq name \"" + seq_name + "\" not unique" )
end
normalized_id = per_species_counter.to_s( 16 ).upcase +
per_species_counter.to_i
- ids_map_writer.write( normalized_id + ": " + seq.get_name + Constants::LINE_DELIMITER )
+ ids_map_writer.write( normalized_id + "\t" + seq.get_name + Constants::LINE_DELIMITER )
orig_name = nil
if seq != nil
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
end
-
-
end
if ( species_code_to_path.has_value?( path ) )
Util.fatal_error( PRG_NAME, "error: path [#{path}] is not unique" )
end
- if ( !File.exist?( path ) )
+ unless ( File.exist?( path ) )
Util.fatal_error( PRG_NAME, "error: file [#{path}] does not exist" )
end
- if ( !File.file?( path ) )
+ unless ( File.file?( path ) )
Util.fatal_error( PRG_NAME, "error: [#{path}] is not a regular file" )
end
- if ( !File.readable?( path ) )
+ unless ( File.readable?( path ) )
Util.fatal_error( PRG_NAME, "error: file [#{path}] is not readable" )
end
- if ( File.size( path ) < 10000 )
+ if ( File.size( path ) < 1000 )
Util.fatal_error( PRG_NAME, "error: file [#{path}] appears too small" )
end
- if ( !Util.looks_like_fasta?( path ) )
+ unless ( Util.looks_like_fasta?( path ) )
Util.fatal_error( PRG_NAME, "error: file [#{path}] does not appear to be a fasta file" )
end
species_code_to_path[ species ] = path
end
def print_counts( per_species_counter, log, ld )
- puts " [sum: " + per_species_counter.to_s + "]"
- log << " [sum: " + per_species_counter.to_s + "]" + ld
+ puts " sum: " + per_species_counter.to_s
+ log << " sum: " + per_species_counter.to_s + ld
end
def read_fasta_file( input )
+ if @file_to_msa.has_key?( input )
+ return @file_to_msa[ input ]
+ end
+
f = MsaFactory.new()
msa = nil
begin
rescue Exception => e
Util.fatal_error( PRG_NAME, "error: " + e.to_s )
end
+ if @seqs <= 400000
+ @file_to_msa[ input ] = msa
+ @seqs += msa.get_number_of_seqs
+ puts " total seqs in memory: " + @seqs.to_s
+ end
msa
end
def print_help()
puts( "Usage:" )
puts()
- puts( " " + PRG_NAME + ".rb <sequence names file suffix> <input dir containing sequence names files " +
- "and possibly genome multiple-sequence ('fasta') files> <output directory for sequences> <output directory for domains> [mapping file for " +
- "genome multiple-sequence ('fasta') files not in input dir]" )
+ puts( " " + PRG_NAME + ".rb <sequence id ('prot') files suffix> <dir containing sequence id ('prot') files>" +
+ " <output directory for protein sequences> <output directory for domain sequences> <genome locations file>" )
puts()
puts( " option: -" + EXT_OPTION + "=<int>: to extend extracted domains" )
puts( " -" + EXTRACT_LINKERS_OPTION + " : to extract linkers" )
git://source.jalview.org / jalview.git / blobdiff