#!/bin/sh
# 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 .
#
#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)
BARCODE_FILE="$1"
FASTQ_FILE="$2"
LIBNAME="$3"
OUTPUT_PATH="$4"
shift 4
# The rest of the parameters are passed to the split program
if [ "$OUTPUT_PATH" == "" ]; then
echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2
exit 1
fi
#Sanitize library name, make sure we can create a file with this name
LIBNAME=${LIBNAME//\.gz/}
LIBNAME=${LIBNAME//\.txt/}
LIBNAME=${LIBNAME//[^[: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=".txt"
RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
if [ $? != 0 ]; then
echo "error"
fi
#
# Convert the textual tab-separated table into simple HTML table,
# with the local path replaces with a valid URL
echo "
"
echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|\\1|" | sed '
i