Mercurial > repos > idot > fastx_toolkit2
comparison fastx_barcode_splitter_galaxy_wrapper.sh @ 0:78a7d28f2a15 draft
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| author | idot |
|---|---|
| date | Wed, 10 Jul 2013 06:13:48 -0400 |
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| -1:000000000000 | 0:78a7d28f2a15 |
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| 1 #!/bin/sh | |
| 2 | |
| 3 # FASTX-toolkit - FASTA/FASTQ preprocessing tools. | |
| 4 # Copyright (C) 2009 A. Gordon (gordon@cshl.edu) | |
| 5 # | |
| 6 # This program is free software: you can redistribute it and/or modify | |
| 7 # it under the terms of the GNU Affero General Public License as | |
| 8 # published by the Free Software Foundation, either version 3 of the | |
| 9 # License, or (at your option) any later version. | |
| 10 # | |
| 11 # This program is distributed in the hope that it will be useful, | |
| 12 # but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| 14 # GNU Affero General Public License for more details. | |
| 15 # | |
| 16 # You should have received a copy of the GNU Affero General Public License | |
| 17 # along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 18 | |
| 19 # | |
| 20 #This is a shell script wrapper for 'fastx_barcode_splitter.pl' | |
| 21 # | |
| 22 # 1. Output files are saved at the dataset's files_path directory. | |
| 23 # | |
| 24 # 2. 'fastx_barcode_splitter.pl' outputs a textual table. | |
| 25 # This script turns it into pretty HTML with working URL | |
| 26 # (so lazy users can just click on the URLs and get their files) | |
| 27 | |
| 28 if [ "$1x" = "x" ]; then | |
| 29 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 | |
| 30 exit 1 | |
| 31 fi | |
| 32 | |
| 33 BARCODE_FILE="$1" | |
| 34 FASTQ_FILE="$2" | |
| 35 LIBNAME="$3" | |
| 36 OUTPUT_PATH="$4" | |
| 37 shift 4 | |
| 38 # The rest of the parameters are passed to the split program | |
| 39 | |
| 40 if [ "${OUTPUT_PATH}x" = "x" ]; then | |
| 41 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2 | |
| 42 exit 1 | |
| 43 fi | |
| 44 | |
| 45 #Sanitize library name, make sure we can create a file with this name | |
| 46 LIBNAME=${LIBNAME%.gz} | |
| 47 LIBNAME=${LIBNAME%.txt} | |
| 48 LIBNAME=$(echo "$LIBNAME" | tr -cd '[:alnum:]') | |
| 49 | |
| 50 if [ ! -r "$FASTQ_FILE" ]; then | |
| 51 echo "Error: Input file ($FASTQ_FILE) not found!" >&2 | |
| 52 exit 1 | |
| 53 fi | |
| 54 if [ ! -r "$BARCODE_FILE" ]; then | |
| 55 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2 | |
| 56 exit 1 | |
| 57 fi | |
| 58 mkdir -p "$OUTPUT_PATH" | |
| 59 if [ ! -d "$OUTPUT_PATH" ]; then | |
| 60 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2 | |
| 61 exit 1 | |
| 62 fi | |
| 63 | |
| 64 PUBLICURL="" | |
| 65 BASEPATH="$OUTPUT_PATH/" | |
| 66 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__" | |
| 67 PREFIX="$BASEPATH""${LIBNAME}__" | |
| 68 SUFFIX=".txt" | |
| 69 | |
| 70 RESULTS=`gzip -cdf "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"` | |
| 71 if [ $? != 0 ]; then | |
| 72 echo "error" | |
| 73 fi | |
| 74 | |
| 75 # | |
| 76 # Convert the textual tab-separated table into simple HTML table, | |
| 77 # with the local path replaces with a valid URL | |
| 78 echo "<html><body><table border=1>" | |
| 79 echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|<a href=\"\\1\">\\1</a>|" | sed ' | |
| 80 i<tr><td> | |
| 81 s|\t|</td><td>|g | |
| 82 a<\/td><\/tr> | |
| 83 ' | |
| 84 echo "<p>" | |
| 85 echo "</table></body></html>" |