64 lines
1.9 KiB
Text
64 lines
1.9 KiB
Text
|
$!
|
||
|
$!VAX-VMS cc make file for readseq
|
||
|
$!
|
||
|
$ echo := write sys$output
|
||
|
$ if p1.eqs."TEST" then goto tests
|
||
|
$
|
||
|
$ echo "compiling readseq..."
|
||
|
$ cc readseq, ureadseq
|
||
|
$!
|
||
|
$ echo "linking readseq..."
|
||
|
$ link readseq, ureadseq, sys$library:vaxcrtl/lib
|
||
|
$!
|
||
|
$tests:
|
||
|
$!
|
||
|
$ echo "defining readseq symbol:"
|
||
|
$ dd = f$environment("default")
|
||
|
$ readseq :== $ 'dd'readseq.exe
|
||
|
$ show symbol readseq
|
||
|
$!
|
||
|
$ echo ""
|
||
|
$ echo "test for general read/write of all chars:"
|
||
|
$ readseq -p alphabet.std -otest.alpha
|
||
|
$ diff test.alpha alphabet.std
|
||
|
$!
|
||
|
$ echo ""
|
||
|
$ echo "test for valid format conversions"
|
||
|
$!
|
||
|
$ readseq -v -p -f=ig nucleic.std -otest.ig
|
||
|
$ readseq -v -p -f=gb test.ig -otest.gb
|
||
|
$ readseq -v -p -f=nbrf test.gb -otest.nbrf
|
||
|
$ readseq -v -p -f=embl test.nbrf -otest.embl
|
||
|
$ readseq -v -p -f=gcg test.embl -otest.gcg
|
||
|
$ readseq -v -p -f=strider test.gcg -otest.strider
|
||
|
$ readseq -v -p -f=fitch test.strider -otest.fitch
|
||
|
$ readseq -v -p -f=fasta test.fitch -otest.fasta
|
||
|
$ readseq -v -p -f=pir test.fasta -otest.pir
|
||
|
$ readseq -v -p -f=ig test.pir -otest.ig-b
|
||
|
$ diff test.ig test.ig-b
|
||
|
$!
|
||
|
$ echo ""
|
||
|
$ echo "Test for multiple-sequence format conversions:"
|
||
|
$ readseq -p -f=ig multi.std -otest.m-ig
|
||
|
$ readseq -p -f=gb test.m-ig -otest.m-gb
|
||
|
$ readseq -p -f=nbrf test.m-gb -otest.m-nbrf
|
||
|
$ readseq -p -f=embl test.m-nbrf -otest.m-embl
|
||
|
$ readseq -p -f=fasta test.m-embl -otest.m-fasta
|
||
|
$ readseq -p -f=pir test.m-fasta -otest.m-pir
|
||
|
$ readseq -p -f=msf test.m-pir -otest.m-msf
|
||
|
$ readseq -p -f=paup test.m-msf -otest.m-paup
|
||
|
$ readseq -p -f=ig test.m-paup -otest.m-ig-b
|
||
|
$ diff test.m-ig test.m-ig-b
|
||
|
$ echo ""
|
||
|
$ echo "Expect differences in the header lines due to"
|
||
|
$ echo "different format headers. If any sequence lines"
|
||
|
$ echo "differ, or if checksums differ, there is a problem."
|
||
|
$!
|
||
|
$! #cleanup
|
||
|
$! delete test.*;
|
||
|
$ echo "-----------"
|
||
|
$ echo ""
|
||
|
$ echo "To clean up test files, command me:
|
||
|
$ echo " DELETE test.*;"
|
||
|
$!
|