runHTSeq.sh
#!
# run from within "repo" directory
EXPERIMENT=$1
SAMPLEID=$2
commandNAME=runHTSeq
if [ ! -d $EXPERIMENT/analyzed/$SAMPLEID/log ]; then
mkdir $EXPERIMENT/analyzed/$SAMPLEID/log
fi
JOURNAL=$EXPERIMENT/analyzed/$SAMPLEID/log/$(date +%Y-%m-%d_%H-%M).$commandNAME.log
if [ ! -d $EXPERIMENT/analyzed/$SAMPLEID/htseq ]; then
mkdir $EXPERIMENT/analyzed/$SAMPLEID/htseq
fi
inputFile="$EXPERIMENT/analyzed/$SAMPLEID/htseq/$SAMPLEID.nameSorted.mateFixed.sam"
gtfFile="resources/htseq/hg19/hg19.gtf"
countsOutFile="$EXPERIMENT/analyzed/$SAMPLEID/htseq/$SAMPLEID.htseq.stdout"
logOutFile="$EXPERIMENT/analyzed/$SAMPLEID/htseq/$SAMPLEID.htseq.stderr"
htseqCommand="python -m HTSeq.scripts.count \
--idattr=gene_id \
--mode=union \
--stranded=no \
--type=exon \
--order=name \
$inputFile \
$gtfFile \
1> $countsOutFile \
2> $logOutFile"
echo "Starting..." >> $JOURNAL
date >> $JOURNAL
echo "$htseqCommand" >> $JOURNAL
eval "$htseqCommand"
date >> $JOURNAL
echo "Done" >> $JOURNAL