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|
#!/bin/bash
# check if all files for utr-training are there before train with utr-modell
workDir=$1
# check if augustus.gff and augustus.gtf exist, make augustus.gtf if it's possible and necessary
cd ${workDir}/predictions/hints.E.1
if [ ! -f augustus.gff ]
then
echo "Can not find the file ${workDir}/predictions/hints.E.1/augustus.gff"
exit 1
elif [ ! -f augustus.gtf ]
then
grep AUGUSTUS augustus.gff > augustus.gtf
fi
# check if ${workDir}/seq/genome.fa exists
cd ${workDir}
cd ${workDir}/seq
if [ ! -f genome.fa ]
then
echo "Can not find the file ${workDir}/seq/genome.fa."
exit 2
fi
# check if cdna.f.psl exists
cd ${workDir}/cdna/alignments
if [ ! -f cdna.f.psl ]
then
echo "Can not find the file ${workDir}/cdna/alignments/cdna.f.psl"
exit 3
fi
# check if training.gb.train.test and training.gb.onlytrain exist
cd ${workDir}/training
if [ ! -f training.gb.train.test ]
then
echo "Can not find ${workDir}/training/training.gb.train.test"
exit 4
elif [ ! -f training.gb.onlytrain ]
then
echo "Can not find ${workDir}/training/training.gb.onlytrain"
exit 5
fi
# if no error, exit with 6
exit 6
|
