gem-merge

#!/bin/bash

SOFTWARE=$1
LAYOUT=$2

set -e

# remove "empty" inputs
for F in `ls *.fpkm`; do
        SIZE=`du -sb $F | cut -f 1`
        if [ $SIZE -lt 50 ]; then
                echo "Removing $F due to it being empty"
                rm $F
        fi
done

echo
echo
ls -l
echo
echo

# no input files left
COUNT=`ls *.fpkm 2>/dev/null | wc -l`
if [ $COUNT = 0 ]; then
    echo "No fpmk files left - creating an empty .tab"
    touch merged_GEM.tab
    exit 0
fi

# move all the input files into a subdir
mkdir inputs
mv *.fpkm inputs/

perl GEM_merge.pl inputs/ > merged_GEM.tab

python Log_merge.py $SOFTWARE $LAYOUT >> QC_Report.tab