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
|
#! /bin/sh
# Usage:
# ./i4-zerolength-seqs.sh <builddir> <srcdir> <HMM database> <tmpfile prefix>
#
# Example:
# ../src/hmmbuild minifam.hmm minifam
# ../src/hmmpress minifam.hmm
# ./i4-zerolength-seqs.sh .. .. minifam.hmm baz
# rm minifam.hmm*
#
# Verifies that the search programs can take zero length sequences as
# input without crashing.
#
# The <HMM database> must be press'ed, for hmmscan to work on it.
if test ! $# -eq 4; then
echo "Usage: $0 <builddir> <srcdir> <HMM database> <tmpfile prefix>"
exit 1
fi
builddir=$1;
srcdir=$2;
hmmfile=$3;
tmppfx=$4;
hmmscan=$builddir/src/hmmscan; if test ! -x $hmmscan; then echo "FAIL: $hmmscan not executable"; exit 1; fi
hmmsearch=$builddir/src/hmmsearch; if test ! -x $hmmsearch; then echo "FAIL: $hmmsearch not executable"; exit 1; fi
phmmer=$builddir/src/phmmer; if test ! -x $phmmer; then echo "FAIL: $phmmer not executable"; exit 1; fi
jackhmmer=$builddir/src/jackhmmer; if test ! -x $jackhmmer; then echo "FAIL: $jackhmmer not executable"; exit 1; fi
if test ! -r $hmmfile; then echo "FAIL: $hmmfile not readable"; exit 1; fi
fafile=$tmppfx.fa
cat > $fafile <<EOF
>foo
>bar
YYYYY
EOF
$hmmscan $hmmfile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi
$hmmsearch $hmmfile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi
$phmmer $fafile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi
$jackhmmer $fafile $fafile > /dev/null 2>&1; if test $? -ne 0; then echo "FAIL: crash"; exit 1; fi
echo "ok"
rm $fafile
exit 0
|
