|
0
|
1 #/bin/bash
|
|
|
2 # Galaxy wrapper script for rDiff version 0.3
|
|
|
3 # Copyright (C) 2013 cBio Department Memorial Sloan-Kettering Cancer Center
|
|
|
4
|
|
|
5 #Licence Information: GPL
|
|
|
6 #This program is free software; you can redistribute it and/or modify
|
|
|
7 #it under the terms of the GNU General Public License as published by
|
|
|
8 #the Free Software Foundation; either version 3 of the License, or
|
|
|
9 #(at your option) any later version
|
|
|
10
|
|
|
11 set -e
|
|
|
12
|
|
|
13 PROG=`basename $0`
|
|
|
14 DIR=`dirname $0`
|
|
|
15 . ${DIR}/../bin/rdiff_config.sh
|
|
|
16
|
|
|
17 echo
|
|
|
18 echo ${PROG}: This program is part of the rDiff version $RDIFF_VERSION.
|
|
|
19 echo
|
|
|
20 echo rDiff performs differential expression testing from RNA-Seq measurements.
|
|
|
21 echo
|
|
|
22
|
|
|
23 if [ -z "$1" -o "$1" == '--help' ];
|
|
|
24 then
|
|
|
25 echo Usage: $0 poisson\|param\|nonparam in.gff readLength out.resultfile out_result_dir S1_in.bam?:S2_in.bam?:
|
|
|
26 echo " :" $0 poisson\|param\|nonparam in.gff readLength out.resultfile out_result_dir S1_R1_in.bam?S1_R2_in.bam?:S2_R1_in.bam?S2_R2_in.bam?:
|
|
|
27 echo " or:" $0 --help
|
|
|
28 echo
|
|
|
29 false
|
|
|
30 fi
|
|
|
31
|
|
|
32 if [ "$1" != 'poisson' -a "$1" != 'param' -a "$1" != 'nonparam' ];
|
|
|
33 then
|
|
|
34 echo invalid parameter: $1
|
|
|
35 echo
|
|
|
36 echo "For usage:" $0 --help
|
|
|
37 false
|
|
|
38 fi
|
|
|
39
|
|
|
40 TEST_METH=$1 ## Test method
|
|
|
41 shift
|
|
|
42 GFF_INPUT=$1 ## Genome annotation in GFF format
|
|
|
43 shift
|
|
|
44 readlength=$1 ## Sequencing read length
|
|
|
45 shift
|
|
|
46 RDIFF_OUT=$1 ## rDiff result file
|
|
|
47 shift
|
|
|
48 RDIFF_OUT_PATH=$1 ## temp session working directory
|
|
|
49 shift
|
|
|
50
|
|
|
51 if [ -d $RDIFF_OUT_PATH ]
|
|
|
52 then
|
|
|
53 echo "Using the extra file path as : $RDIFF_OUT_PATH"
|
|
|
54 else
|
|
|
55 mkdir -p ${RDIFF_OUT_PATH} ## create the temp working directory
|
|
|
56 fi
|
|
|
57
|
|
|
58 ## changing tool working directory to the session path
|
|
|
59 cd ${RDIFF_OUT_PATH}
|
|
|
60
|
|
|
61 ## Seperating the files according to the sample and correspondinf replicates.
|
|
|
62 SAMPLE_LIST=()
|
|
|
63 for SAMPLES in $@
|
|
|
64 do
|
|
|
65 IFS='?'
|
|
|
66 for BAM_FILE in ${SAMPLES}
|
|
|
67 do
|
|
|
68 if [ $BAM_FILE = ":" ]; ## samples are seperated with ':'
|
|
|
69 then
|
|
|
70 SAMPLE_LIST+=(${SAMPLE_FNAME%?}) ## samples are separating
|
|
|
71 SAMPLE_FNAME=""
|
|
|
72 continue
|
|
|
73 fi
|
|
|
74 if [ ! -f ${BAM_FILE}.bai ]
|
|
|
75 then
|
|
|
76 echo "Indexing $BAM_FILE"
|
|
|
77 ${RDIFF_SAMTOOLS_INCLUDE_DIR}/samtools index $BAM_FILE
|
|
|
78 else
|
|
|
79 echo "$BAM_FILE already indexed"
|
|
|
80 fi
|
|
|
81 La_fn=$BAM_FILE
|
|
|
82 SAMPLE_FNAME="$SAMPLE_FNAME$BAM_FILE," ## adding a ',' between each BAM files.
|
|
|
83 done
|
|
|
84 done
|
|
|
85
|
|
|
86 ## rDiff execution call
|
|
|
87 ${DIR}/../bin/rdiff -o ${RDIFF_OUT_PATH} -d / -g ${GFF_INPUT} -a ${SAMPLE_LIST[0]} -b ${SAMPLE_LIST[1]} -m ${TEST_METH} -L ${readlength}
|
|
|
88
|
|
|
89 ## rdiff out file
|
|
|
90 ln -fs ${RDIFF_OUT_PATH}/P_values_rDiff_"${TEST_METH/param/parametric}".tab ${RDIFF_OUT}
|
