From: cmzmasek Date: Mon, 27 Mar 2017 22:11:58 +0000 (-0700) Subject: in progress... X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9f8ca1a5901b832746b856673eb0eedbf7f2d432;p=jalview.git in progress... --- diff --git a/forester/ruby/evoruby/lib/evo/msa/msa.rb b/forester/ruby/evoruby/lib/evo/msa/msa.rb index a355d19..2d2f93b 100644 --- a/forester/ruby/evoruby/lib/evo/msa/msa.rb +++ b/forester/ruby/evoruby/lib/evo/msa/msa.rb @@ -533,7 +533,7 @@ module Evoruby seq = get_sequence(i) name = seq.get_name() # >sp|Q1HVE7|AN_EBVA8 Shutoff alkaline exonuclease OS=Epstein-Barr virus (strain AG876) GN=BGLF5 PE=3 SV=1 - # if name =~ /OS=(.+?)\s+[A-Z]{2}=/ + # if name =~ /OS=(.+?)\s+[A-Z]{2}=/ if name =~ /Organism:(.+?)(\|Protein|$)/ os = $1 unless msa_hash.has_key?(os) @@ -541,16 +541,16 @@ module Evoruby end msa_hash[os].add_sequence seq else - error_msg = "sequence name \"" + name +"\" is not in the expected format for splitting by OS" + error_msg = "sequence name \"" + name + "\" is not in the expected format for splitting by OS" raise IOError, error_msg, caller end end msa_hash = msa_hash.sort{|a, b|a<=>b}.to_h if verbose c = 0 - msa_hash.each do |os, msa| + msa_hash.each do |o, msa| c += 1 - puts c.to_s + ': ' + os + puts c.to_s + ': ' + o end end msa_hash diff --git a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb index 77935cd..04caba8 100644 --- a/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb +++ b/forester/ruby/evoruby/lib/evo/tool/multi_sequence_extractor.rb @@ -5,7 +5,6 @@ # License:: GNU Lesser General Public License (LGPL) # - require 'lib/evo/util/constants' require 'lib/evo/util/util' require 'lib/evo/msa/msa' @@ -16,15 +15,12 @@ require 'lib/evo/io/writer/fasta_writer' require 'lib/evo/util/command_line_arguments' module Evoruby - class MultiSequenceExtractor PRG_NAME = "mse" PRG_VERSION = "1.04" - PRG_DESC = "extraction of sequences by name from multiple multi-sequence ('fasta') files" - PRG_DATE = "140318" - COPYRIGHT = "2014 Christian M Zmasek" - CONTACT = "phyloxml@gmail.com" + PRG_DESC = "processing of \"surfacing\" output: extraction of sequences by name from multiple multi-sequence ('fasta') files" + PRG_DATE = "170327" WWW = "https://sites.google.com/site/cmzmasek/home/software/forester" HELP_OPTION_1 = 'help' HELP_OPTION_2 = 'h' @@ -37,7 +33,6 @@ module Evoruby FASTA_WITH_NORMALIZED_IDS_SUFFIX = ".ni.fasta" NORMALIZED_IDS_MAP_SUFFIX = ".nim" PROTEINS_LIST_FILE_SEPARATOR = "\t" - def initialize() @file_to_msa = Hash.new @seqs = 0 @@ -46,13 +41,11 @@ module Evoruby 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 ) ld = Constants::LINE_DELIMITER @@ -63,7 +56,7 @@ module Evoruby 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 @@ -80,8 +73,8 @@ module Evoruby 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 seq_names_files_suffix = cla.get_file_name( 0 ) @@ -92,7 +85,7 @@ module Evoruby begin Util.check_file_for_readability( mapping_file ) - rescue ArgumentError => e + rescue IOError => e Util.fatal_error( PRG_NAME, "error: " + e.to_s ) end @@ -175,24 +168,6 @@ module Evoruby puts puts counter.to_s + "/" + input_files.size.to_s read_seq_family_file( input_file, - seq_names_files_suffix, - input_dir, - species_codes_to_paths, - log, - out_dir, - out_dir_doms, - mapping_file, - extension, - extract_linkers ) - } - puts - Util.print_message( PRG_NAME, "OK" ) - puts - - end - - - def read_seq_family_file( input_file, seq_names_files_suffix, input_dir, species_codes_to_paths, @@ -202,6 +177,23 @@ module Evoruby mapping_file, extension, extract_linkers ) + } + puts + Util.print_message( PRG_NAME, "OK" ) + puts + + end + + def read_seq_family_file( input_file, + seq_names_files_suffix, + input_dir, + species_codes_to_paths, + log, + out_dir, + out_dir_doms, + mapping_file, + extension, + extract_linkers ) begin Util.check_file_for_readability( input_file ) @@ -212,10 +204,10 @@ module Evoruby out_file_path_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX out_file_path_normalized_ids_fasta_file = out_dir + Constants::FILE_SEPARATOR + basename + FASTA_WITH_NORMALIZED_IDS_SUFFIX out_file_path_ids_map = out_dir + Constants::FILE_SEPARATOR + basename + NORMALIZED_IDS_MAP_SUFFIX - doms_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains" + FASTA_SUFFIX + doms_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + FASTA_SUFFIX doms_ext_out_file_path_fasta_file = nil if extension > 0 - doms_ext_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_domains_ext_" + extension.to_s + FASTA_SUFFIX + doms_ext_out_file_path_fasta_file = out_dir_doms + Constants::FILE_SEPARATOR + basename + "_ext_" + extension.to_s + FASTA_SUFFIX end begin Util.check_file_for_writability( out_file_path_fasta_file ) @@ -255,9 +247,7 @@ module Evoruby 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 + seq_name = values[ 1 ] domain_ranges = nil if ( values.length > 3 ) @@ -310,7 +300,7 @@ module Evoruby end normalized_id = per_species_counter.to_s( 16 ).upcase + - "_" + current_species + "_" + current_species per_species_counter.to_i @@ -335,11 +325,11 @@ module Evoruby from = s[ 0 ].to_i to = s[ 1 ].to_i new_msa_domains.add_sequence( Sequence.new( orig_name + - " [" + from.to_s + - "-" + to.to_s + - "] [" + basename + "] [" + - current_species + "]", - seq.get_sequence_as_string[from..to] ) ) + " [" + from.to_s + + "-" + to.to_s + + "] [" + basename + "] [" + + current_species + "]", + seq.get_sequence_as_string[from..to] ) ) if extension > 0 from_e = from - extension if from_e < 0 @@ -350,13 +340,13 @@ module Evoruby to_e = seq.get_sequence_as_string.length - 1 end new_msa_domains_extended.add_sequence( Sequence.new( orig_name + - " [" + from.to_s + - "-" + to.to_s + - "] [extended by " + - extension.to_s + - "] [" + basename + "] [" + - current_species + "]", - seq.get_sequence_as_string[ from_e..to_e ] ) ) + " [" + from.to_s + + "-" + to.to_s + + "] [extended by " + + extension.to_s + + "] [" + basename + "] [" + + current_species + "]", + seq.get_sequence_as_string[ from_e..to_e ] ) ) end # extension > 0 if extract_linkers if first @@ -452,7 +442,6 @@ module Evoruby end end - def get_linker_sequence( from, to, seq ) if from < 0 from = 0 @@ -544,12 +533,13 @@ module Evoruby puts( "Usage:" ) puts() puts( " " + PRG_NAME + ".rb " + - " " ) + " " ) puts() puts( " option: -" + EXT_OPTION + "=: to extend extracted domains" ) puts( " -" + EXTRACT_LINKERS_OPTION + " : to extract linkers" ) puts() - puts( " " + "Example: \"mse.rb .prot . protein_seqs domain_seqs ../genome_locations.txt\"" ) + puts( " " + "Examples: mse.rb .prot . protein_seqs domain_seqs ../genome_locations.txt" ) + puts( " " + " mse.rb .prot . FL_seqs DA_seqs ../../genome_locations.txt" ) puts() end