fastx_barcode_splitter_enhanced: fastx_barcode

annotate fastx_barcode_splitter.pl @ 1:b7b3d008e2d3 draft

planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastx_barcode_splitter_enhanced commit e6a486662201362134119c0ddc7151b8dd181ebd

author	lparsons
date	Tue, 27 Oct 2015 11:47:52 -0400
parents	84bbf4fd24c3
children	e7b7cdc1834d

rev	line source
0 84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	1 #!/usr/bin/perl
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	2
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	3 # FASTX-toolkit - FASTA/FASTQ preprocessing tools.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	4 # Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	5 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	6 # Lance Parsons (lparsons@princeton.edu)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	7 # 3/21/2011 - Modified to accept separate index file for barcodes
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	8 # 4/6/2011 - Modified to cleanup bad barcode identifiers (esp. useful for Galaxy)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	9 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	10 # This program is free software: you can redistribute it and/or modify
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	11 # it under the terms of the GNU Affero General Public License as
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	12 # published by the Free Software Foundation, either version 3 of the
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	13 # License, or (at your option) any later version.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	14 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	15 # This program is distributed in the hope that it will be useful,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	16 # but WITHOUT ANY WARRANTY; without even the implied warranty of
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	18 # GNU Affero General Public License for more details.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	19 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	20 # You should have received a copy of the GNU Affero General Public License
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	21 # along with this program. If not, see <http://www.gnu.org/licenses/>.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	22
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	23 use strict;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	24 use warnings;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	25 use IO::Handle;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	26 use Data::Dumper;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	27 use Getopt::Long;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	28 use Carp;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	29
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	30 ##
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	31 ## This program splits a FASTQ/FASTA file into several smaller files,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	32 ## Based on barcode matching.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	33 ##
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	34 ## run with "--help" for usage information
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	35 ##
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	36 ## Assaf Gordon <gordon@cshl.edu> , 11sep2008
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	37
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	38 # Forward declarations
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	39 sub load_barcode_file ($);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	40 sub parse_command_line ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	41 sub match_sequences ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	42 sub mismatch_count($$) ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	43 sub print_results;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	44 sub open_and_detect_input_format;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	45 sub open_index_and_detect_input_format($);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	46 sub read_index_record;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	47 sub read_record;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	48 sub write_record($);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	49 sub usage();
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	50
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	51 # Global flags and arguments,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	52 # Set by command line argumens
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	53 my $barcode_file ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	54 my $barcodes_at_eol = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	55 my $barcodes_at_bol = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	56 my $index_read_file ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	57 my $exact_match = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	58 my $allow_partial_overlap = 0;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	59 my $allowed_mismatches = 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	60 my $newfile_suffix = '';
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	61 my $newfile_prefix ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	62 my $quiet = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	63 my $debug = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	64 my $fastq_format = 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	65 my $index_fastq_format = 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	66 my $read_id_check_strip_characters = 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	67
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	68 # Global variables
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	69 # Populated by 'create_output_files'
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	70 my %filenames;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	71 my %files;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	72 my %counts = ( 'unmatched' => 0 );
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	73 my $barcodes_length;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	74 my @barcodes;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	75 my $input_file_io;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	76
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	77
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	78 # The Four lines per record in FASTQ format.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	79 # (when using FASTA format, only the first two are used)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	80 my $seq_name;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	81 my $seq_bases;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	82 my $seq_name2;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	83 my $seq_qualities;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	84
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	85 # Values used for index read file
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	86 my $index_seq_name;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	87 my $index_seq_bases;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	88 my $index_seq_name2;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	89 my $index_seq_qualities;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	90
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	91
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	92
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	93 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	94 # Start of Program
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	95 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	96 parse_command_line ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	97
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	98 load_barcode_file ( $barcode_file ) ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	99
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	100 open_and_detect_input_format;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	101
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	102 if (defined $index_read_file) {open_index_and_detect_input_format ( $index_read_file );}
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	103
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	104 match_sequences ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	105
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	106 print_results unless $quiet;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	107
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	108 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	109 # End of program
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	110 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	111
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	112
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	113
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	114
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	115
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	116
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	117
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	118
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	119 sub parse_command_line {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	120 my $help;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	121
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	122 usage() if (scalar @ARGV==0);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	123
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	124 my $result = GetOptions ( "bcfile=s" => \$barcode_file,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	125 "eol" => \$barcodes_at_eol,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	126 "bol" => \$barcodes_at_bol,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	127 "idxfile=s" => \$index_read_file,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	128 "idxidstrip=i" => \$read_id_check_strip_characters,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	129 "exact" => \$exact_match,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	130 "prefix=s" => \$newfile_prefix,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	131 "suffix=s" => \$newfile_suffix,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	132 "quiet" => \$quiet,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	133 "partial=i" => \$allow_partial_overlap,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	134 "debug" => \$debug,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	135 "mismatches=i" => \$allowed_mismatches,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	136 "help" => \$help
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	137 ) ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	138
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	139 usage() if ($help);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	140
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	141 die "Error: barcode file not specified (use '--bcfile [FILENAME]')\n" unless defined $barcode_file;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	142 die "Error: prefix path/filename not specified (use '--prefix [PATH]')\n" unless defined $newfile_prefix;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	143
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	144 if (! defined $index_read_file) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	145 if ($barcodes_at_bol == $barcodes_at_eol) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	146 die "Error: can't specify both --eol & --bol\n" if $barcodes_at_eol;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	147 die "Error: must specify either --eol or --bol or --idxfile\n" ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	148 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	149 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	150 elsif ($barcodes_at_bol \|\| $barcodes_at_eol) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	151 die "Error: Must specify only one of --idxfile, --eol, or --bol";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	152 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	153
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	154 die "Error: invalid for value partial matches (valid values are 0 or greater)\n" if $allow_partial_overlap<0;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	155
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	156 $allowed_mismatches = 0 if $exact_match;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	157
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	158 die "Error: invalid value for mismatches (valid values are 0 or more)\n" if ($allowed_mismatches<0);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	159
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	160 die "Error: partial overlap value ($allow_partial_overlap) bigger than " .
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	161 "max. allowed mismatches ($allowed_mismatches)\n" if ($allow_partial_overlap > $allowed_mismatches);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	162
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	163
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	164 exit unless $result;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	165 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	166
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	167
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	168
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	169 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	170 # Read the barcode file
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	171 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	172 sub load_barcode_file ($) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	173 my $filename = shift or croak "Missing barcode file name";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	174
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	175 open BCFILE,"<$filename" or die "Error: failed to open barcode file ($filename)\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	176 while (<BCFILE>) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	177 next if m/^#/;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	178 chomp;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	179 my ($ident, $barcode) = split('\t') ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	180
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	181 $barcode = uc($barcode);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	182
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	183 # Sanity checks on the barcodes
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	184 die "Error: bad data at barcode file ($filename) line $.\n" unless defined $barcode;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	185 die "Error: bad barcode value ($barcode) at barcode file ($filename) line $.\n"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	186 unless $barcode =~ m/^[AGCT]+$/;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	187
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	188 # Cleanup Identifiers (only allow alphanumeric, replace others with dash '-')
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	189 $ident =~ s/[^A-Za-z0-9]/-/g;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	190 die "Error: bad identifier value ($ident) at barcode file ($filename) line $. (must be alphanumeric)\n"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	191 unless $ident =~ m/^[A-Za-z0-9-]+$/;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	192
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	193 die "Error: badcode($ident, $barcode) is shorter or equal to maximum number of " .
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	194 "mismatches ($allowed_mismatches). This makes no sense. Specify fewer mismatches.\n"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	195 if length($barcode)<=$allowed_mismatches;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	196
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	197 $barcodes_length = length($barcode) unless defined $barcodes_length;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	198 die "Error: found barcodes in different lengths. this feature is not supported yet.\n"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	199 unless $barcodes_length == length($barcode);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	200
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	201 push @barcodes, [$ident, $barcode];
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	202
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	203 if ($allow_partial_overlap>0) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	204 foreach my $i (1 .. $allow_partial_overlap) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	205 substr $barcode, ($barcodes_at_bol)?0:-1, 1, '';
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	206 push @barcodes, [$ident, $barcode];
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	207 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	208 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	209 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	210 close BCFILE;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	211
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	212 if ($debug) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	213 print STDERR "barcode\tsequence\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	214 foreach my $barcoderef (@barcodes) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	215 my ($ident, $seq) = @{$barcoderef};
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	216 print STDERR $ident,"\t", $seq ,"\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	217 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	218 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	219 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	220
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	221 # Create one output file for each barcode.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	222 # (Also create a file for the dummy 'unmatched' barcode)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	223 sub create_output_files {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	224 my %barcodes = map { $_->[0] => 1 } @barcodes; #generate a uniq list of barcode identifiers;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	225 $barcodes{'unmatched'} = 1 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	226
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	227 foreach my $ident (keys %barcodes) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	228 my $new_filename = $newfile_prefix . $ident . $newfile_suffix;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	229 $filenames{$ident} = $new_filename;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	230 open my $file, ">$new_filename" or die "Error: failed to create output file ($new_filename)\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	231 $files{$ident} = $file ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	232 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	233 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	234
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	235 sub match_sequences {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	236
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	237 my %barcodes = map { $_->[0] => 1 } @barcodes; #generate a uniq list of barcode identifiers;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	238 $barcodes{'unmatched'} = 1 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	239
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	240 #reset counters
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	241 foreach my $ident ( keys %barcodes ) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	242 $counts{$ident} = 0;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	243 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	244
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	245 create_output_files;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	246
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	247 # Read file FASTQ file
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	248 # split accotding to barcodes
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	249 while ( read_record ) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	250 chomp $seq_name;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	251 chomp $seq_bases;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	252 if (defined $index_read_file) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	253 read_index_record() or die "Error: Unable to read index sequence for sequence name ($seq_name), check to make sure the file lengths match.\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	254 chomp $index_seq_name;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	255 chomp $index_seq_bases;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	256
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	257 # Assert that the read ids match
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	258 my $seq_name_match = &strip_read_id($seq_name);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	259 my $index_seq_name_match = &strip_read_id($index_seq_name);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	260 if ($seq_name_match ne $index_seq_name_match) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	261 die "Error: Index sequence name ($index_seq_name) does not match sequence name ($seq_name)\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	262 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	263
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	264 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	265
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	266 print STDERR "sequence $seq_bases: \n" if $debug;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	267
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	268 my $best_barcode_mismatches_count = $barcodes_length;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	269 my $best_barcode_ident = undef;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	270
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	271 #Try all barcodes, find the one with the lowest mismatch count
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	272 foreach my $barcoderef (@barcodes) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	273 my ($ident, $barcode) = @{$barcoderef};
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	274
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	275 # Get DNA fragment (in the length of the barcodes)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	276 # The barcode will be tested only against this fragment
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	277 # (no point in testing the barcode against the whole sequence)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	278 my $sequence_fragment;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	279 if ($barcodes_at_bol) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	280 $sequence_fragment = substr $seq_bases, 0, $barcodes_length;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	281 } elsif ($barcodes_at_eol) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	282 $sequence_fragment = substr $seq_bases, - $barcodes_length;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	283 } else {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	284 $sequence_fragment = substr $index_seq_bases, 0, $barcodes_length;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	285 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	286
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	287 my $mm = mismatch_count($sequence_fragment, $barcode) ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	288
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	289 # if this is a partial match, add the non-overlap as a mismatch
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	290 # (partial barcodes are shorter than the length of the original barcodes)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	291 $mm += ($barcodes_length - length($barcode));
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	292
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	293 if ( $mm < $best_barcode_mismatches_count ) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	294 $best_barcode_mismatches_count = $mm ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	295 $best_barcode_ident = $ident ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	296 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	297 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	298
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	299 $best_barcode_ident = 'unmatched'
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	300 if ( (!defined $best_barcode_ident) \|\| $best_barcode_mismatches_count>$allowed_mismatches) ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	301
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	302 print STDERR "sequence $seq_bases matched barcode: $best_barcode_ident\n" if $debug;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	303
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	304 $counts{$best_barcode_ident}++;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	305
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	306 #get the file associated with the matched barcode.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	307 #(note: there's also a file associated with 'unmatched' barcode)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	308 my $file = $files{$best_barcode_ident};
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	309
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	310 write_record($file);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	311 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	312 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	313
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	314 # Strip end of readids when matching to avoid mismatch between read 1, 2, 3, etc.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	315 sub strip_read_id {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	316 my $read_id = shift;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	317 my $stripped_read_id = $read_id;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	318 if ($read_id_check_strip_characters) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	319 if ($read_id =~ /@([a-zA-Z0-9_-]+):([0-9]+):([a-zA-Z0-9]+):([0-9]+):([0-9]+):([0-9]+):([0-9]+) ([0-9]+):([YN]):([0-9]+):([ACGT]+){0,1}/) { # CASAVA 1.8+
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	320 my @parts = split(/ /,$read_id);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	321 $stripped_read_id = $parts[0];
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	322 } else { # CASAVA 1.7 and earlier
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	323 $stripped_read_id = substr($read_id, 0, length($read_id)-$read_id_check_strip_characters);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	324 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	325 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	326 return $stripped_read_id;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	327 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	328
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	329
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	330 #Quickly calculate hamming distance between two strings
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	331 #
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	332 #NOTE: Strings must be same length.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	333 # returns number of different characters.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	334 #see http://www.perlmonks.org/?node_id=500235
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	335 sub mismatch_count($$) { length( $_[ 0 ] ) - ( ( $_[ 0 ] ^ $_[ 1 ] ) =~ tr[\0][\0] ) }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	336
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	337
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	338
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	339 sub print_results
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	340 {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	341 print "Barcode\tCount\tLocation\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	342 my $total = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	343 foreach my $ident (sort keys %counts) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	344 print $ident, "\t", $counts{$ident},"\t",$filenames{$ident},"\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	345 $total += $counts{$ident};
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	346 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	347 print "total\t",$total,"\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	348 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	349
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	350
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	351 sub read_record
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	352 {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	353 $seq_name = $input_file_io->getline();
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	354
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	355 return undef unless defined $seq_name; # End of file?
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	356
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	357 $seq_bases = $input_file_io->getline();
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	358 die "Error: bad input file, expecting line with sequences\n" unless defined $seq_bases;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	359
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	360 # If using FASTQ format, read two more lines
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	361 if ($fastq_format) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	362 $seq_name2 = $input_file_io->getline();
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	363 die "Error: bad input file, expecting line with sequence name2\n" unless defined $seq_name2;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	364
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	365 $seq_qualities = $input_file_io->getline();
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	366 die "Error: bad input file, expecting line with quality scores\n" unless defined $seq_qualities;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	367 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	368 return 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	369 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	370
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	371 sub write_record($)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	372 {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	373 my $file = shift;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	374
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	375 croak "Bad file handle" unless defined $file;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	376
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	377 print $file $seq_name,"\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	378 print $file $seq_bases,"\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	379
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	380 #if using FASTQ format, write two more lines
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	381 if ($fastq_format) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	382 print $file $seq_name2;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	383 print $file $seq_qualities;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	384 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	385 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	386
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	387 sub open_and_detect_input_format
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	388 {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	389 $input_file_io = new IO::Handle;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	390 die "Failed to open STDIN " unless $input_file_io->fdopen(fileno(STDIN),"r");
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	391
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	392 # Get the first characeter, and push it back
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	393 my $first_char = $input_file_io->getc();
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	394 $input_file_io->ungetc(ord $first_char);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	395
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	396 if ($first_char eq '>') {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	397 # FASTA format
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	398 $fastq_format = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	399 print STDERR "Detected FASTA format\n" if $debug;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	400 } elsif ($first_char eq '@') {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	401 # FASTQ format
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	402 $fastq_format = 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	403 print STDERR "Detected FASTQ format\n" if $debug;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	404 } else {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	405 die "Error: unknown file format. First character = '$first_char' (expecting > or \@)\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	406 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	407 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	408
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	409
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	410 sub open_index_and_detect_input_format($) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	411 my $filename = shift or croak "Missing index read file name";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	412
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	413 open IDXFILE,"<$filename" or die "Error: failed to open index read file ($filename)\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	414
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	415 # Get the first line, and reset file pointer
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	416 my $first_line = <IDXFILE>;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	417 my $first_char = substr($first_line, 0, 1);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	418 seek(IDXFILE, 0, 0);
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	419
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	420 if ($first_char eq '>') {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	421 # FASTA format
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	422 $index_fastq_format = 0 ;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	423 print STDERR "Detected FASTA format for index file\n" if $debug;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	424 } elsif ($first_char eq '@') {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	425 # FASTQ format
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	426 $index_fastq_format = 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	427 print STDERR "Detected FASTQ format for index file\n" if $debug;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	428 } else {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	429 die "Error: unknown index file format. First character = '$first_char' (expecting > or \@)\n";
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	430 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	431 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	432
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	433 sub read_index_record
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	434 {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	435 $index_seq_name = <IDXFILE>;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	436
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	437 return undef unless defined $index_seq_name; # End of file?
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	438
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	439 $index_seq_bases = <IDXFILE>;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	440 die "Error: bad input file, expecting line with sequences\n" unless defined $index_seq_bases;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	441
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	442 # If using FASTQ format, read two more lines
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	443 if ($index_fastq_format) {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	444 $index_seq_name2 = <IDXFILE>;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	445 die "Error: bad input file, expecting line with sequence name2\n" unless defined $index_seq_name2;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	446
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	447 $index_seq_qualities = <IDXFILE>;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	448 die "Error: bad input file, expecting line with quality scores\n" unless defined $index_seq_qualities;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	449 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	450 return 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	451 }
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	452
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	453 sub usage()
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	454 {
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	455 print<<EOF;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	456 Barcode Splitter, by Assaf Gordon (gordon\@cshl.edu), 11sep2008
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	457
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	458 This program reads FASTA/FASTQ file and splits it into several smaller files,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	459 Based on barcode matching.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	460 FASTA/FASTQ data is read from STDIN (format is auto-detected.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	461 Output files will be writen to disk.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	462 Summary will be printed to STDOUT.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	463
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	464 usage: $0 --bcfile FILE --prefix PREFIX [--suffix SUFFIX] [--bol\|--eol\|--idxfile]
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	465 [--mismatches N] [--exact] [--partial N] [--idxidstrip N]
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	466 [--help] [--quiet] [--debug]
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	467
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	468 Arguments:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	469
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	470 --bcfile FILE - Barcodes file name. (see explanation below.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	471 --prefix PREFIX - File prefix. will be added to the output files. Can be used
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	472 to specify output directories.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	473 --suffix SUFFIX - File suffix (optional). Can be used to specify file
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	474 extensions.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	475 --bol - Try to match barcodes at the BEGINNING of sequences.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	476 (What biologists would call the 5' end, and programmers
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	477 would call index 0.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	478 --eol - Try to match barcodes at the END of sequences.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	479 (What biologists would call the 3' end, and programmers
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	480 would call the end of the string.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	481 --idxfile FILE - Read barcodes from separate index file (fasta or fastq)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	482 NOTE: one of --bol, --eol, --idxfile must be specified,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	483 but not more than one.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	484 --idxidstrip N - When using index file, strip this number of characters
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	485 from the end of the sequence id before matching.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	486 Automatically detects CASAVA 1.8 format and strips at a
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	487 space in the id, use 0 to disable this.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	488 (Default is 1).
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	489 --mismatches N - Max. number of mismatches allowed. default is 1.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	490 --exact - Same as '--mismatches 0'. If both --exact and --mismatches
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	491 are specified, '--exact' takes precedence.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	492 --partial N - Allow partial overlap of barcodes. (see explanation below.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	493 (Default is not partial matching)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	494 --quiet - Don't print counts and summary at the end of the run.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	495 (Default is to print.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	496 --debug - Print lots of useless debug information to STDERR.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	497 --help - This helpful help screen.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	498
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	499 Example (Assuming 's_2_100.txt' is a FASTQ file, 'mybarcodes.txt' is
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	500 the barcodes file):
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	501
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	502 \$ cat s_2_100.txt \| $0 --bcfile mybarcodes.txt --bol --mismatches 2 \\
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	503 --prefix /tmp/bla_ --suffix ".txt"
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	504
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	505 Barcode file format
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	506 -------------------
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	507 Barcode files are simple text files. Each line should contain an identifier
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	508 (descriptive name for the barcode), and the barcode itself (A/C/G/T),
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	509 separated by a TAB character. Example:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	510
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	511 #This line is a comment (starts with a 'number' sign)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	512 BC1 GATCT
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	513 BC2 ATCGT
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	514 BC3 GTGAT
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	515 BC4 TGTCT
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	516
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	517 For each barcode, a new FASTQ file will be created (with the barcode's
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	518 identifier as part of the file name). Sequences matching the barcode
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	519 will be stored in the appropriate file.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	520
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	521 Running the above example (assuming "mybarcodes.txt" contains the above
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	522 barcodes), will create the following files:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	523 /tmp/bla_BC1.txt
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	524 /tmp/bla_BC2.txt
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	525 /tmp/bla_BC3.txt
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	526 /tmp/bla_BC4.txt
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	527 /tmp/bla_unmatched.txt
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	528 The 'unmatched' file will contain all sequences that didn't match any barcode.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	529
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	530 Barcode matching
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	531 ----------------
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	532
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	533 ** Without partial matching:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	534
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	535 Count mismatches between the FASTA/Q sequences and the barcodes.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	536 The barcode which matched with the lowest mismatches count (providing the
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	537 count is small or equal to '--mismatches N') 'gets' the sequences.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	538
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	539 Example (using the above barcodes):
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	540 Input Sequence:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	541 GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	542
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	543 Matching with '--bol --mismatches 1':
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	544 GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	545 GATCT (1 mismatch, BC1)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	546 ATCGT (4 mismatches, BC2)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	547 GTGAT (3 mismatches, BC3)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	548 TGTCT (3 mismatches, BC4)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	549
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	550 This sequence will be classified as 'BC1' (it has the lowest mismatch count).
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	551 If '--exact' or '--mismatches 0' were specified, this sequence would be
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	552 classified as 'unmatched' (because, although BC1 had the lowest mismatch count,
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	553 it is above the maximum allowed mismatches).
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	554
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	555 Matching with '--eol' (end of line) does the same, but from the other side
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	556 of the sequence.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	557
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	558 ** With partial matching (very similar to indels):
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	559
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	560 Same as above, with the following addition: barcodes are also checked for
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	561 partial overlap (number of allowed non-overlapping bases is '--partial N').
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	562
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	563 Example:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	564 Input sequence is ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	565 (Same as above, but note the missing 'G' at the beginning.)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	566
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	567 Matching (without partial overlapping) against BC1 yields 4 mismatches:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	568 ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	569 GATCT (4 mismatches)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	570
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	571 Partial overlapping would also try the following match:
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	572 -ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	573 GATCT (1 mismatch)
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	574
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	575 Note: scoring counts a missing base as a mismatch, so the final
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	576 mismatch count is 2 (1 'real' mismatch, 1 'missing base' mismatch).
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	577 If running with '--mismatches 2' (meaning allowing upto 2 mismatches) - this
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	578 seqeunce will be classified as BC1.
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	579
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	580 EOF
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	581
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	582 exit 1;
84bbf4fd24c3 Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. lparsons parents: diff changeset	583 }

Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

annotate fastx_barcode_splitter.pl @ 1:b7b3d008e2d3 draft