| Next changeset 1:b7b3d008e2d3 (2015-10-27) |
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Commit message:
Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history. |
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added:
fastx_barcode_splitter.pl fastx_barcode_splitter.xml fastx_barcode_splitter_galaxy_wrapper.sh test-data/fastx_barcode_splitter1.fastq test-data/fastx_barcode_splitter1.out test-data/fastx_barcode_splitter1.txt |
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| diff -r 000000000000 -r 84bbf4fd24c3 fastx_barcode_splitter.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_barcode_splitter.pl Fri Nov 08 09:53:39 2013 -0500 |
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| b'@@ -0,0 +1,583 @@\n+#!/usr/bin/perl\n+\n+# FASTX-toolkit - FASTA/FASTQ preprocessing tools.\n+# Copyright (C) 2009 A. Gordon (gordon@cshl.edu)\n+#\n+# Lance Parsons (lparsons@princeton.edu)\n+# 3/21/2011 - Modified to accept separate index file for barcodes\n+# 4/6/2011 - Modified to cleanup bad barcode identifiers (esp. useful for Galaxy)\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU Affero General Public License as\n+# published by the Free Software Foundation, either version 3 of the\n+# License, or (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n+# GNU Affero General Public License for more details.\n+#\n+# You should have received a copy of the GNU Affero General Public License\n+# along with this program. If not, see <http://www.gnu.org/licenses/>.\n+\n+use strict;\n+use warnings;\n+use IO::Handle;\n+use Data::Dumper;\n+use Getopt::Long;\n+use Carp;\n+\n+##\n+## This program splits a FASTQ/FASTA file into several smaller files,\n+## Based on barcode matching.\n+##\n+## run with "--help" for usage information\n+##\n+## Assaf Gordon <gordon@cshl.edu> , 11sep2008\n+\n+# Forward declarations\n+sub load_barcode_file ($);\n+sub parse_command_line ;\n+sub match_sequences ;\n+sub mismatch_count($$) ;\n+sub print_results;\n+sub open_and_detect_input_format;\n+sub open_index_and_detect_input_format($);\n+sub read_index_record;\n+sub read_record;\n+sub write_record($);\n+sub usage();\n+\n+# Global flags and arguments, \n+# Set by command line argumens\n+my $barcode_file ;\n+my $barcodes_at_eol = 0 ;\n+my $barcodes_at_bol = 0 ;\n+my $index_read_file ;\n+my $exact_match = 0 ;\n+my $allow_partial_overlap = 0;\n+my $allowed_mismatches = 1;\n+my $newfile_suffix = \'\';\n+my $newfile_prefix ;\n+my $quiet = 0 ;\n+my $debug = 0 ;\n+my $fastq_format = 1;\n+my $index_fastq_format = 1;\n+my $read_id_check_strip_characters = 1;\n+\n+# Global variables \n+# Populated by \'create_output_files\'\n+my %filenames;\n+my %files;\n+my %counts = ( \'unmatched\' => 0 );\n+my $barcodes_length;\n+my @barcodes;\n+my $input_file_io;\n+\n+\n+# The Four lines per record in FASTQ format.\n+# (when using FASTA format, only the first two are used)\n+my $seq_name;\n+my $seq_bases;\n+my $seq_name2;\n+my $seq_qualities;\n+\n+# Values used for index read file\n+my $index_seq_name;\n+my $index_seq_bases;\n+my $index_seq_name2;\n+my $index_seq_qualities;\n+\n+\n+\n+#\n+# Start of Program\n+#\n+parse_command_line ;\n+\n+load_barcode_file ( $barcode_file ) ;\n+\n+open_and_detect_input_format;\n+\n+if (defined $index_read_file) {open_index_and_detect_input_format ( $index_read_file );}\n+\n+match_sequences ;\n+\n+print_results unless $quiet;\n+\n+#\n+# End of program\n+#\n+\n+\n+\n+\n+\n+\n+\n+\n+sub parse_command_line {\n+\tmy $help;\n+\n+\tusage() if (scalar @ARGV==0);\n+\n+\tmy $result = GetOptions ( "bcfile=s" => \\$barcode_file,\n+\t\t"eol" => \\$barcodes_at_eol,\n+\t\t"bol" => \\$barcodes_at_bol,\n+\t\t"idxfile=s" => \\$index_read_file,\n+\t\t"idxidstrip=i" => \\$read_id_check_strip_characters,\n+\t\t"exact" => \\$exact_match,\n+\t\t"prefix=s" => \\$newfile_prefix,\n+\t\t"suffix=s" => \\$newfile_suffix,\n+\t\t"quiet" => \\$quiet, \n+\t\t"partial=i" => \\$allow_partial_overlap,\n+\t\t"debug" => \\$debug,\n+\t\t"mismatches=i" => \\$allowed_mismatches,\n+\t\t"help" => \\$help\n+\t) ;\n+\n+\tusage() if ($help);\n+\n+\tdie "Error: barcode file not specified (use \'--bcfile [FILENAME]\')\\n" unless defined $barcode_file;\n+\tdie "Error: prefix path/filename not specified (use \'--prefix [PATH]\')\\n" unless defined $newfile_prefix;\n+\n+\tif (! defined $index_read_file) {\n+\t\tif ($barcodes_at_bol == $barcodes_at_eol) {\n+\t\t\tdie "Error: can\'t specify both --eol & --bol\\n" if $barcodes_at_eol;\n+\t\t\tdie "Error: must specify either --eol or --bol or --idxfile\\n" ;\n+\t\t}\n+\t}\n+\telsif ($barcodes_at_bol || $barcodes_at_eol) {\n+\t\tdie "Error: Must specify only one of --idxfile, --eol, or'..b'ists would call the 5\' end, and programmers\n+\t\t would call index 0.)\n+--eol\t\t- Try to match barcodes at the END of sequences.\n+\t\t (What biologists would call the 3\' end, and programmers\n+\t\t would call the end of the string.)\n+--idxfile FILE - Read barcodes from separate index file (fasta or fastq)\n+\t\t NOTE: one of --bol, --eol, --idxfile must be specified,\n+\t\t but not more than one.\n+--idxidstrip N - When using index file, strip this number of characters\n+\t\t from the end of the sequence id before matching.\n+\t\t Automatically detects CASAVA 1.8 format and strips at a\n+\t\t space in the id, use 0 to disable this.\n+\t\t (Default is 1). \n+--mismatches N\t- Max. number of mismatches allowed. default is 1.\n+--exact\t\t- Same as \'--mismatches 0\'. If both --exact and --mismatches \n+\t\t are specified, \'--exact\' takes precedence.\n+--partial N\t- Allow partial overlap of barcodes. (see explanation below.)\n+\t\t (Default is not partial matching)\n+--quiet\t\t- Don\'t print counts and summary at the end of the run.\n+\t\t (Default is to print.)\n+--debug\t\t- Print lots of useless debug information to STDERR.\n+--help\t\t- This helpful help screen.\n+\n+Example (Assuming \'s_2_100.txt\' is a FASTQ file, \'mybarcodes.txt\' is \n+the barcodes file):\n+\n+ \\$ cat s_2_100.txt | $0 --bcfile mybarcodes.txt --bol --mismatches 2 \\\\\n+\t--prefix /tmp/bla_ --suffix ".txt"\n+\n+Barcode file format\n+-------------------\n+Barcode files are simple text files. Each line should contain an identifier \n+(descriptive name for the barcode), and the barcode itself (A/C/G/T), \n+separated by a TAB character. Example:\n+\n+ #This line is a comment (starts with a \'number\' sign)\n+ BC1 GATCT\n+ BC2 ATCGT\n+ BC3 GTGAT\n+ BC4 TGTCT\n+\n+For each barcode, a new FASTQ file will be created (with the barcode\'s \n+identifier as part of the file name). Sequences matching the barcode \n+will be stored in the appropriate file.\n+\n+Running the above example (assuming "mybarcodes.txt" contains the above \n+barcodes), will create the following files:\n+\t/tmp/bla_BC1.txt\n+\t/tmp/bla_BC2.txt\n+\t/tmp/bla_BC3.txt\n+\t/tmp/bla_BC4.txt\n+\t/tmp/bla_unmatched.txt\n+The \'unmatched\' file will contain all sequences that didn\'t match any barcode.\n+\n+Barcode matching\n+----------------\n+\n+** Without partial matching:\n+\n+Count mismatches between the FASTA/Q sequences and the barcodes.\n+The barcode which matched with the lowest mismatches count (providing the\n+count is small or equal to \'--mismatches N\') \'gets\' the sequences.\n+\n+Example (using the above barcodes):\n+Input Sequence:\n+GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG\n+\n+Matching with \'--bol --mismatches 1\':\n+GATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG\n+GATCT (1 mismatch, BC1)\n+ATCGT (4 mismatches, BC2)\n+GTGAT (3 mismatches, BC3)\n+TGTCT (3 mismatches, BC4)\n+\n+This sequence will be classified as \'BC1\' (it has the lowest mismatch count).\n+If \'--exact\' or \'--mismatches 0\' were specified, this sequence would be \n+classified as \'unmatched\' (because, although BC1 had the lowest mismatch count,\n+it is above the maximum allowed mismatches).\n+\n+Matching with \'--eol\' (end of line) does the same, but from the other side\n+of the sequence.\n+\n+** With partial matching (very similar to indels):\n+\n+Same as above, with the following addition: barcodes are also checked for\n+partial overlap (number of allowed non-overlapping bases is \'--partial N\').\n+\n+Example:\n+Input sequence is ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG\n+(Same as above, but note the missing \'G\' at the beginning.)\n+\n+Matching (without partial overlapping) against BC1 yields 4 mismatches:\n+ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG\n+GATCT (4 mismatches)\n+\n+Partial overlapping would also try the following match:\n+-ATTTACTATGTAAAGATAGAAGGAATAAGGTGAAG\n+GATCT (1 mismatch)\n+\n+Note: scoring counts a missing base as a mismatch, so the final\n+mismatch count is 2 (1 \'real\' mismatch, 1 \'missing base\' mismatch).\n+If running with \'--mismatches 2\' (meaning allowing upto 2 mismatches) - this \n+seqeunce will be classified as BC1.\n+\n+EOF\n+\n+exit 1;\n+}\n' |
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| diff -r 000000000000 -r 84bbf4fd24c3 fastx_barcode_splitter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_barcode_splitter.xml Fri Nov 08 09:53:39 2013 -0500 |
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| @@ -0,0 +1,92 @@ +<tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True"> + <description></description> + <command interpreter="bash"> + fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial + #if $refBarcodeLocation.barcodeLocation == "idxfile": + --idxfile $refBarcodeLocation.idxfile + #else: + $refBarcodeLocation.EOL + #end if + > $output + </command> + + <inputs> + <param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" /> + <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" /> + + <conditional name="refBarcodeLocation"> + <param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at"> + <option value="bol">Start of sequence (5' end)</option> + <option value="eol">End of sequence (3' end)</option> + <option value="idxfile">Separate index file</option> + </param> + <when value="bol"> + <param version="1.1" name="EOL" type="hidden" value="--bol" /> + </when> + <when value="eol"> + <param version="1.1" name="EOL" type="hidden" value="--eol" /> + </when> + <when value="idxfile"> + <param version="1.1" name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" /> + </when> + </conditional> + + <param version="1.1" name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" /> + + <param version="1.1" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> + + </inputs> + + <tests> + <test> + <!-- Split a FASTQ file --> + <param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" /> + <param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> + <param version="1.1" name="EOL" value="Start of sequence (5' end)" /> + <param version="1.1" name="mismatches" value="2" /> + <param version="1.1" name="partial" value="0" /> + <output version="1.1" name="output" file="fastx_barcode_splitter1.out" /> + </test> + </tests> + + <outputs> + <data version="1.1" format="html" name="output" /> + </outputs> +<help> + +**What it does** + +This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria. + +-------- + +**Barcode file Format** + +Barcode files are simple text files. +Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. +Example:: + + #This line is a comment (starts with a 'number' sign) + BC1 GATCT + BC2 ATCGT + BC3 GTGAT + BC4 TGTCT + +For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). +Sequences matching the barcode will be stored in the appropriate file. + +One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. + +The output of this tool is an HTML file, displaying the split counts and the file names. +In addition, each fastq file produced will be loaded into the galaxy history automatically. + + +------ + +This tool is based on `FASTX-toolkit`__ by Assaf Gordon. + + .. __: http://hannonlab.cshl.edu/fastx_toolkit/ + +</help> +<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> +</tool> |
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| diff -r 000000000000 -r 84bbf4fd24c3 fastx_barcode_splitter_galaxy_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastx_barcode_splitter_galaxy_wrapper.sh Fri Nov 08 09:53:39 2013 -0500 |
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| @@ -0,0 +1,90 @@ +#!/bin/bash + +# FASTX-toolkit - FASTA/FASTQ preprocessing tools. +# Copyright (C) 2009 A. Gordon (gordon@cshl.edu) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +# Modified by Lance Parsons (lparsons@princeton.edu) +# 2011-03-15 Adapted to allow galaxy to determine filetype +# +#This is a shell script wrapper for 'fastx_barcode_splitter.pl' +# +# 1. Output files are saved at the dataset's files_path directory. +# +# 2. 'fastx_barcode_splitter.pl' outputs a textual table. +# This script turns it into pretty HTML with working URL +# (so lazy users can just click on the URLs and get their files) + +if [ "$1x" = "x" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 + exit 1 +fi + +BARCODE_FILE="$1" +FASTQ_FILE="$2" +LIBNAME="$3" +OUTPUT_PATH="$4" +FILETYPE="$5" +shift 5 +# The rest of the parameters are passed to the split program + +if [ "${OUTPUT_PATH}x" = "x" ]; then + echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH] [FILETYPE]" >&2 + exit 1 +fi + +#Sanitize library name, make sure we can create a file with this name +LIBNAME=${LIBNAME%.gz} +LIBNAME=${LIBNAME%.txt} +LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]_') + +if [ ! -r "$FASTQ_FILE" ]; then + echo "Error: Input file ($FASTQ_FILE) not found!" >&2 + exit 1 +fi +if [ ! -r "$BARCODE_FILE" ]; then + echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 + exit 1 +fi +mkdir -p "$OUTPUT_PATH" +if [ ! -d "$OUTPUT_PATH" ]; then + echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 + exit 1 +fi + +PUBLICURL="" +BASEPATH="$OUTPUT_PATH/" +#PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" +PREFIX="$BASEPATH""${LIBNAME}_" +SUFFIX="_visible_$FILETYPE" +DIRECTORY=$(cd `dirname $0` && pwd) + +RESULTS=`gzip -cdf "$FASTQ_FILE" | $DIRECTORY/fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` +if [ $? != 0 ]; then + echo "error" +fi + +# +# Convert the textual tab-separated table into simple HTML table, +# with the local path replaces with a valid URL +#HTMLSUMMARY=${PREFIX}stats_visible_html +echo "<html><body><table border=1>" +echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed ' +i<tr><td> +s|\t|</td><td>|g +a<\/td><\/tr> +' +echo "<p>" +echo "</table></body></html>" |
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| diff -r 000000000000 -r 84bbf4fd24c3 test-data/fastx_barcode_splitter1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_barcode_splitter1.fastq Fri Nov 08 09:53:39 2013 -0500 |
| b |
| @@ -0,0 +1,168 @@ +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GATCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTAGTAGTAGTAGA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGTACGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCGTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +ATCTCGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +GGAATGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TAGTTTCTCTATGTACA ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa +@CSHL_3_FC042AGLLWW:1:2:7:203 +TGTCTGAGTATACACAT ++CSHL_3_FC042AGLLWW:1:2:7:203 +aab^V^aU]`aa^aZaa \ No newline at end of file |
| b |
| diff -r 000000000000 -r 84bbf4fd24c3 test-data/fastx_barcode_splitter1.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_barcode_splitter1.out Fri Nov 08 09:53:39 2013 -0500 |
| b |
| @@ -0,0 +1,24 @@ +<html><body><table border=1> +<tr><td> +Barcode</td><td>Count</td><td>Location +</td></tr> +<tr><td> +BC1</td><td>11</td><td><a href="fastx_barcode_splitter1_fastq__BC1.txt">fastx_barcode_splitter1_fastq__BC1.txt</a> +</td></tr> +<tr><td> +BC2</td><td>12</td><td><a href="fastx_barcode_splitter1_fastq__BC2.txt">fastx_barcode_splitter1_fastq__BC2.txt</a> +</td></tr> +<tr><td> +BC3</td><td>9</td><td><a href="fastx_barcode_splitter1_fastq__BC3.txt">fastx_barcode_splitter1_fastq__BC3.txt</a> +</td></tr> +<tr><td> +BC4</td><td>1</td><td><a href="fastx_barcode_splitter1_fastq__BC4.txt">fastx_barcode_splitter1_fastq__BC4.txt</a> +</td></tr> +<tr><td> +unmatched</td><td>9</td><td><a href="fastx_barcode_splitter1_fastq__unmatched.txt">fastx_barcode_splitter1_fastq__unmatched.txt</a> +</td></tr> +<tr><td> +total</td><td>42 +</td></tr> +<p> +</table></body></html> |
| b |
| diff -r 000000000000 -r 84bbf4fd24c3 test-data/fastx_barcode_splitter1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastx_barcode_splitter1.txt Fri Nov 08 09:53:39 2013 -0500 |
| b |
| @@ -0,0 +1,4 @@ +BC1 GATCT +BC2 ATCGT +BC3 GTGAT +BC4 TGTCT \ No newline at end of file |