Mercurial > repos > lparsons > fastx_barcode_splitter_enhanced

#!/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
#	2015-10-21	Updated to make compatible with OSX (BSD sed)
#   2015-11-13  Removed LIBRARY_NAME, no longer needed

#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] [OUTPUT_PATH] [FILETYPE]" >&2
	exit 1
fi

BARCODE_FILE="$1"
FASTQ_FILE="$2"
OUTPUT_PATH="$3"
FILETYPE="$4"
shift 4
# The rest of the parameters are passed to the split program

if [ "${OUTPUT_PATH}x" = "x" ]; then
	echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [OUTPUT_PATH] [FILETYPE]" >&2
	exit 1
fi

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

BASEPATH="$OUTPUT_PATH/"
PREFIX="$BASEPATH"
SUFFIX=".$FILETYPE"
DIRECTORY="$(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
echo "<html><body><table border=1>"
echo "$RESULTS" | sed "s|$BASEPATH\\(.*\\)|\\1|" | \
perl -n -e '$_ =~ s|\t|</td><td>|g; print "<tr><td>\n$_</td></tr>\n"'
echo "<p>"
echo "</table></body></html>"
author	lparsons
date	Fri, 11 Mar 2016 17:24:31 -0500
parents	32304398ef67
children	0fb7e9130a70