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