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#! /bin/sh
## Inits
align=$srcdir/align/phylips.seq
## Check default PHYLIPS file reference
(../src/squizz -A -f phylips $align 2>&1 | grep -v PHYLIPS) && exit 1
## Check for sequences on a single line (= PHYLIPI)
grep -v '^$' $align | grep -v '^ ' >_tmpali.seq
(../src/squizz -A -f phylips _tmpali.seq 2>&1 | grep -v PHYLIPS) && 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 phylips _tmpali.seq 2>&1 | grep PHYLIPS) && exit 1
## Check sequence names with spaces
sed 's,\., ,' $align >_tmpali.seq
(../src/squizz -A -f phylips _tmpali.seq 2>&1 | grep -v PHYLIPS) && exit 1
## Check without newline at EOF
sed -e '$d' $align >_tmpali.seq
tail -n 1 $align | tr -d '\n' >>_tmpali.seq
(../src/squizz -A -f phylips _tmpali.seq 2>&1 | grep -v PHYLIPS) && exit 1
## Cleanup
rm -f _tmpali.seq
exit 0
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