added inversionfix.py and variantfilter.py to installation

parent 59e10822
.DELETE_ON_ERROR:
dist_bin_SCRIPTS = biodiff \
udiff2vcf
udiff2vcf \
inversionfix.py \
variantfilter.py
PANDOC = @PANDOC@
......
......@@ -56,7 +56,7 @@ fi
isolatenpath=${query%.fasta} # get isolate ID by stripping suffix
isolate=${isolatenpath##*/} # and stripping path
dnadiff -p $tmpdir/$isolate $reference $query
../../inversionfix.py -r $tmpdir/$isolate.rdiff -q $tmpdir/$isolate.qdiff -v $tmpdir/$isolate-temp.vcf -f $query -p $reference -t $tmpdir/$isolate-temp.fasta
inversionfix.py -r $tmpdir/$isolate.rdiff -q $tmpdir/$isolate.qdiff -v $tmpdir/$isolate-temp.vcf -f $query -p $reference -t $tmpdir/$isolate-temp.fasta
# inversionfix.py will need to be made an exacutable in the path eventually
read_fasta "$refdir" $reference
......@@ -90,6 +90,6 @@ EOF
diff -irdb -U1 "$refdir" "$qrydir" \
| udiff2vcf >> $tmpdir/$isolate-temp.vcf # append output of diff to temp.vcf file, which has the inversion calls
python ../../variantfilter.py -i $tmpdir/$isolate-temp.vcf -o $tmpdir/$isolate-temp-filtered.vcf
variantfilter.py -i $tmpdir/$isolate-temp.vcf -o $tmpdir/$isolate-temp-filtered.vcf
sort -k2 -n $tmpdir/$isolate-temp-filtered.vcf # sort by position, and output to stdout
......@@ -4,5 +4,6 @@ tests=$(ls "$DATADIR" | grep -v reference.fasta)
for item in $tests
do
echo "Checking lambda $item"
integration $DATADIR/reference.fasta $DATADIR/$item
done
File mode changed from 100644 to 100755
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