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
|
#! /bin/sh
## Inits
align=$srcdir/align/phylipi.seq
## Check default PHYLIPI file reference
(../src/squizz -A -f phylipi $align 2>&1 | grep -v PHYLIPI) && exit 1
## Check format name aliases
(../src/squizz -A -f phylip $align 2>&1 | grep -v PHYLIPI) && exit 1
## Check for sequences on a single line (= PHYLIPS)
grep -v '^$' $align | grep -v '^ ' >_tmpali.seq
(../src/squizz -A -f phylipi _tmpali.seq 2>&1 | grep -v PHYLIPI) && exit 1
## Check with empty line after header
echo " 13 109" >_tmpali.seq
echo >>_tmpali.seq
tail -n +2 $align >>_tmpali.seq
(../src/squizz -A -f phylipi _tmpali.seq 2>&1 | grep PHYLIPI) && exit 1
## Check sequence names with spaces
sed 's,ISA, SA,' $align >_tmpali.seq
(../src/squizz -A -f phylipi _tmpali.seq 2>&1 | grep -v PHYLIPI) && exit 1
## Check without newline at EOF
sed -e '$d' $align >_tmpali.seq
tail -n 1 $align | tr -d '\n' >>_tmpali.seq
(../src/squizz -A -f phylipi _tmpali.seq 2>&1 | grep -v PHYLIPI) && exit 1
## Check with extra newlines at EOF
echo | cat $align - >_tmpali.seq
(../src/squizz -A -f phylipi _tmpali.seq 2>&1 | grep -v PHYLIPI) && exit 1
## Cleanup
rm -f _tmpali.seq
exit 0
|
