annotate deseq-hts_1.0/src/deseq-hts.sh @ 11:cec4b4fb30be draft default tip

DEXSeq version 1.6 added
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 08:22:45 -0400
parents e27b4f7811c2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
1 #/bin/bash
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
2 #
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
3 # This program is free software; you can redistribute it and/or modify
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
4 # it under the terms of the GNU General Public License as published by
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
5 # the Free Software Foundation; either version 3 of the License, or
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
6 # (at your option) any later version.
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
7 #
9
e27b4f7811c2 Updated DESeq version 1.12
vipints <vipin@cbio.mskcc.org>
parents: 1
diff changeset
8 # Copyright (C) 2009-2013 Max Planck Society & Memorial Sloan-Kettering Cancer Center
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
9 #
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
10
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
11 set -e
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
12
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
13 PROG=`basename $0`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
14 DIR=`dirname $0`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
15
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
16 . ${DIR}/../bin/deseq_config.sh
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
17
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
18 echo
9
e27b4f7811c2 Updated DESeq version 1.12
vipints <vipin@cbio.mskcc.org>
parents: 1
diff changeset
19 echo ${PROG}: Oqtans http://galaxy.cbio.mskcc.org Galaxy wrapper for the DESeq version $DESEQ_VERSION.
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
20 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
21 echo DESeq performs differential expression testing from RNA-Seq measurements.
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
22 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
23
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
24 ANNO_INPUT=${1}
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
25 shift
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
26 DESEQ_RES_FILE=${1}
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
27 shift
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
28 GENES_FN=${1}
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
29 shift
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
30
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
31 mkdir -p `dirname $GENES_FN`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
32
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
33 echo %%%%%%%%%%%%%%%%%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
34 echo % 1. Data preparation %
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
35 echo %%%%%%%%%%%%%%%%%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
36 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
37 echo load the genome annotation in GFF3 format and create an annotation object
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
38 export PYTHONPATH=$PYTHONPATH:${SCIPY_PATH}
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
39 ${PYTHON_PATH} ${DIR}/../tools/ParseGFF.py ${ANNO_INPUT} ${GENES_FN}
9
e27b4f7811c2 Updated DESeq version 1.12
vipints <vipin@cbio.mskcc.org>
parents: 1
diff changeset
40 ${DIR}/../bin/genes_cell2struct ${GENES_FN}
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
41 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
42 echo genome annotation stored in $GENES_FN
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
43
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
44 echo %%%%%%%%%%%%%%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
45 echo % 2. Read counting %
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
46 echo %%%%%%%%%%%%%%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
47 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
48
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
49 echo counting reads overlapping exons using given alignments
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
50 for REPLICATE_GROUP in $@
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
51 do
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
52 IFS=':'
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
53 for BAM_FILE in ${REPLICATE_GROUP}
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
54 do
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
55 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
56 if [ ! -f ${BAM_FILE}.bai ]
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
57 then
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
58 echo "Indexing $BAM_FILE"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
59 ${SAMTOOLS_DIR}/samtools index $BAM_FILE
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
60 else
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
61 echo "$BAM_FILE already indexed"
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
62 fi
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
63 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
64 done
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
65 done
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
66 tmpfile=`mktemp --tmpdir=/tmp`
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
67
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
68 echo "${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile $@"
9
e27b4f7811c2 Updated DESeq version 1.12
vipints <vipin@cbio.mskcc.org>
parents: 1
diff changeset
69 ${DIR}/../bin/get_read_counts ${GENES_FN} $tmpfile "$@"
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
70
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
71 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
72 echo % 3. Differential testing %
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
73 echo %%%%%%%%%%%%%%%%%%%%%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
74 echo
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
75 echo testing genes for differential expression using given alignments
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
76
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
77 echo "cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $#"
9
e27b4f7811c2 Updated DESeq version 1.12
vipints <vipin@cbio.mskcc.org>
parents: 1
diff changeset
78 cat ${DIR}/../src/difftest_deseq.R | $R_PATH --slave --args $tmpfile ${DESEQ_RES_FILE} $#
0
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
79
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
80 rm $tmpfile ${tmpfile}_COUNTS.tab ${tmpfile}_CONDITIONS.tab
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
81 echo %%%%%%%%
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
82 echo % Done %
94a108763d9e deseq-hts version 1.0 wraps the DESeq 1.6.0
vipints
parents:
diff changeset
83 echo %%%%%%%%