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comparison deseq-hts_1.0/src/deseq-hts.sh @ 9:e27b4f7811c2 draft

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Updated DESeq version 1.12
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:09:28 -0400
parents 8ab01cc29c4b
children
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8:2b3bb3348076 9:e27b4f7811c2
3 # This program is free software; you can redistribute it and/or modify 3 # This program is free software; you can redistribute it and/or modify
4 # it under the terms of the GNU General Public License as published by 4 # it under the terms of the GNU General Public License as published by
5 # the Free Software Foundation; either version 3 of the License, or 5 # the Free Software Foundation; either version 3 of the License, or
6 # (at your option) any later version. 6 # (at your option) any later version.
7 # 7 #
8 # Copyright (C) 2009-2012 Max Planck Society 8 # Copyright (C) 2009-2013 Max Planck Society & Memorial Sloan-Kettering Cancer Center
9 # 9 #
10 10
11 set -e 11 set -e
12 12
13 PROG=`basename $0` 13 PROG=`basename $0`
14 DIR=`dirname $0` 14 DIR=`dirname $0`
15 15
16 . ${DIR}/../bin/deseq_config.sh 16 . ${DIR}/../bin/deseq_config.sh
17 17
18 echo 18 echo
19 echo ${PROG}: FML http://galaxy.fml.mpg.de Galaxy wrapper for the DESeq version $DESEQ_VERSION. 19 echo ${PROG}: Oqtans http://galaxy.cbio.mskcc.org Galaxy wrapper for the DESeq version $DESEQ_VERSION.
20 echo 20 echo
21 echo DESeq performs differential expression testing from RNA-Seq measurements. 21 echo DESeq performs differential expression testing from RNA-Seq measurements.
22 echo 22 echo
23 23
24 ANNO_INPUT=${1} 24 ANNO_INPUT=${1}
33 echo %%%%%%%%%%%%%%%%%%%%%%% 33 echo %%%%%%%%%%%%%%%%%%%%%%%
34 echo % 1. Data preparation % 34 echo % 1. Data preparation %
35 echo %%%%%%%%%%%%%%%%%%%%%%% 35 echo %%%%%%%%%%%%%%%%%%%%%%%
36 echo 36 echo
37 echo load the genome annotation in GFF3 format and create an annotation object 37 echo load the genome annotation in GFF3 format and create an annotation object
38 echo
39 export PYTHONPATH=$PYTHONPATH:${SCIPY_PATH} 38 export PYTHONPATH=$PYTHONPATH:${SCIPY_PATH}
40 ${PYTHON_PATH} ${DIR}/../tools/ParseGFF.py ${ANNO_INPUT} ${GENES_FN} 39 ${PYTHON_PATH} ${DIR}/../tools/ParseGFF.py ${ANNO_INPUT} ${GENES_FN}
41 ${DIR}/../bin/genes_cell2struct ${GENES_FN} 2>&1 40 ${DIR}/../bin/genes_cell2struct ${GENES_FN}
42 echo 41 echo
43 echo genome annotation stored in $GENES_FN 42 echo genome annotation stored in $GENES_FN
44 43
45 echo
46 echo %%%%%%%%%%%%%%%%%%%% 44 echo %%%%%%%%%%%%%%%%%%%%
47 echo % 2. Read counting % 45 echo % 2. Read counting %
48 echo %%%%%%%%%%%%%%%%%%%% 46 echo %%%%%%%%%%%%%%%%%%%%
49 echo 47 echo
50 48
66 done 64 done
67 done 65 done
68 tmpfile=`mktemp --tmpdir=/tmp` 66 tmpfile=`mktemp --tmpdir=/tmp`
69 67
70 echo "${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@" 68 echo "${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@"
71 ${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@" 2>&1 69 ${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@"
72 70
73 echo
74 echo %%%%%%%%%%%%%%%%%%%%%%%%%%% 71 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
75 echo % 3. Differential testing % 72 echo % 3. Differential testing %
76 echo %%%%%%%%%%%%%%%%%%%%%%%%%%% 73 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
77 echo 74 echo
78
79 echo testing genes for differential expression using given alignments 75 echo testing genes for differential expression using given alignments
80 76
81 echo "cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $#" 77 echo "cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $#"
82 cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $# 2> /dev/null 78 cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $#
83 79
84 rm $tmpfile ${tmpfile}_COUNTS.tab ${tmpfile}_CONDITIONS.tab 80 rm $tmpfile ${tmpfile}_COUNTS.tab ${tmpfile}_CONDITIONS.tab
85 echo
86 echo %%%%%%%% 81 echo %%%%%%%%
87 echo % Done % 82 echo % Done %
88 echo %%%%%%%% 83 echo %%%%%%%%
89 echo