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
66
67
68
69
70
71
72
73
74
75
76
|
#! /bin/sh
## Verbose mode
test "x$VERBOSE" = xx && set -x
tmpseq=_convert.seq
## Sequence files location
seqdir=$srcdir/sequence
seqlist='codata.seq embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq nbrf.seq raw.seq refseqn.seq refseqp.seq'
## Checks CODATA-like sequence
for f in $seqlist; do
../src/squizz -c codata $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v CODATA) && exit 1
done
## Checks EMBL-like sequence
for f in $seqlist; do
../src/squizz -c embl $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v EMBL) && exit 1
done
## Checks FASTA-like sequence/alignment
for f in $seqlist; do
../src/squizz -c fasta $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v FASTA) && exit 1
done
## Checks GCG-like sequence
for f in $seqlist; do
../src/squizz -c gcg $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v GCG) && exit 1
done
## Checks GDE-like sequence
for f in $seqlist; do
../src/squizz -c gde $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v GDE) && exit 1
done
## Checks GENBANK-like sequence
for f in $seqlist; do
../src/squizz -c genbank $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v GENBANK) && exit 1
done
## Checks IG-like sequence
for f in $seqlist; do
../src/squizz -c ig $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v IG) && exit 1
done
## Checks NBRF-like sequence
for f in $seqlist; do
../src/squizz -c nbrf $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v NBRF) && exit 1
done
## Checks RAW-like sequence
for f in $seqlist; do
../src/squizz -c raw $seqdir/$f >$tmpseq 2>/dev/null
(../src/squizz $tmpseq 2>&1 | grep -v RAW) && exit 1
done
## Checks SWISSPROT-like sequence
#for f in $seqlist; do
# ../src/squizz -c swissprot $seqdir/$f >$tmpseq 2>/dev/null
# (../src/squizz $tmpseq 2>&1 | grep -v SWISSPROT) && exit 1
#done
## Clean temp files
rm -f $tmpseq
exit 0
|
