|
0
|
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>"
|
