1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
|
#!/bin/bash
set -e
pkg="mummer"
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
find . -name "*.gz" -exec gunzip \{\} \;
mkdir output/ && cd output/
echo "--------promer----"
/usr/bin/promer -p promer ../input/D_melanogaster_2Rslice.fasta ../input/D_pseudoobscura_contigs.fasta
/usr/bin/show-coords -r -c -l -L 100 -I 50 promer.delta > promer.coords
/usr/bin/show-aligns promer.delta "D_melanogaster_2Rslice" "3214968" > promer.aligns
echo "--------mapview----"
/usr/bin/mapview -n 1 -p mapview promer.coords
/usr/bin/mapview -n 1 -p mapview promer.coords ../input/D_melanogaster_2Rslice.utr ../input/D_melanogaster_2Rslice.cds
/usr/bin/mapview -n 1 -f pdf -p mapview promer.coords ../input/D_melanogaster_2Rslice.utr ../input/D_melanogaster_2Rslice.cds
echo "--------mummer----"
/usr/bin/mummer -mum -b -c ../input/H_pylori26695_Eslice.fasta ../input/H_pyloriJ99_Eslice.fasta > mummer.mums
echo "echo"
#/usr/bin/mummerplot -x "[0,275287]" -y "[0,265111]" -postscript -p mummer mummer.mums
echo "--------nucmer----"
/usr/bin/nucmer -maxmatch -c 100 -p nucmer ../input/B_anthracis_Mslice.fasta ../input/B_anthracis_contigs.fasta
/usr/bin/show-coords -r -c -l nucmer.delta > nucmer.coords
/usr/bin/show-snps -C nucmer.delta > nucmer.snps
/usr/bin/show-tiling nucmer.delta > nucmer.tiling
#echo "--------run-mummer1----"
#/usr/bin/run-mummer1 ../input/H_pylori26695_Bslice.fasta ../input/H_pyloriJ99_Bslice.fasta mummer1 -r
echo "--------run-mummer3----"
/usr/bin/run-mummer3 ../input/H_pylori26695_Bslice.fasta ../input/H_pyloriJ99_Bslice.fasta mummer3
#fix output first lines for diffcheck
tail -n +2 nucmer.coords > nucmer.coords
tail -n +2 nucmer.delta > nucmer.delta
tail -n +2 nucmer.snps > nucmer.snps
tail -n +2 promer.aligns > promer.aligns
tail -n +2 promer.coords > promer.coords
tail -n +2 promer.delta > promer.delta
tail -n +2 ../expected/nucmer.coords > ../expected/nucmer.coords
tail -n +2 ../expected/nucmer.delta > ../expected/nucmer.delta
tail -n +2 ../expected/nucmer.snps > ../expected/nucmer.snps
tail -n +2 ../expected/promer.aligns > ../expected/promer.aligns
tail -n +2 ../expected/promer.coords > ../expected/promer.coords
tail -n +2 ../expected/promer.delta > ../expected/promer.delta
cd $AUTOPKGTEST_TMP
for i in `ls expected/|xargs` ; do
diff expected/$i output/$i
done
echo "PASS"
|
