alnmrg.sh
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上传日期:2007-06-13
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文件大小:2k
- #! /bin/sh
- # $Id: alnmrg.sh,v 1000.2 2004/06/01 19:40:55 gouriano Exp $
- #
- unset GENBANK_ID1_STATS
- test_dir="./data"
- tmp_out=$test_dir/out.asn
- return_status=0
- run_prg() {
- $CHECK_EXEC alnmrg -in $test_dir/$1.asn $2 > $tmp_out
- if test "$?" != 0; then
- echo "FAILURE:"
- return_status=1
- fi
- }
- check_diff() {
- cmp -s $test_dir/$1.asn $tmp_out
- if test "$?" != 0; then
- echo "FAILURE: $2"
- return_status=1
- fi
- }
- # in.asn == out.asn
- test1() {
- run_prg "$1" "$2"
- check_diff "$1" "$3"
- }
- # in.asn != out.asn
- test2() {
- run_prg "$1" "$2"
- check_diff "$1.out" "$3"
- }
- #### TEST CASES #####
- test1 unaln "-fillunaln t -noobjmgr t"
- "test that fillunaln does not affect this alignment"
- # gi 6467445
- test2 independent_dss "-b Seq-entry"
- "test independent dss"
- # gi 19880863
- test2 gapjoin "-gapjoin t -b Seq-entry"
- "test gap join"
- # gi 19172277
- test2 19172277 "-b Seq-entry" "test gi 19172277"
- test1 multiple_row_inserts "" "multiple row inserts"
- test2 iterator_minus_minus "" "iterator minus minus"
- # test2 blast "-queryseqmergeonly t" "blast output merge"
- test2 seg_overlap "" "overlapping segments"
- test2 trunc1 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 1"
- test2 trunc2 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 2"
- test2 trunc3 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 3"
- test2 trunc4 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 4"
- test2 trunc5 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 5"
- test2 trunc6 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 6"
- test2 trunc7 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 7"
- test2 trunc8 "-truncateoverlaps t -noobjmgr t" "truncation of overlaps 8"
- rm $tmp_out
- echo "Done!"
- exit $return_status
- #
- # ===========================================================================
- # PRODUCTION $Log: alnmrg.sh,v $
- # PRODUCTION Revision 1000.2 2004/06/01 19:40:55 gouriano
- # PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11
- # PRODUCTION
- # ===========================================================================
- #