Package list tigr-glimmer / 12b2e3f
Add autopkgtests Nilesh Patra 2 years ago
2 changed file(s) with 13 addition(s) and 38 deletion(s). Raw diff Collapse all Expand all
00 Tests: run-unit-test
11 Depends: @
22 Restrictions: allow-stderr
3
00 #!/bin/bash
11 set -e
22
3 pkg="tigr-glimmer"
3 pkg=tigr-glimmer
44
5 if [ "$AUTOPKGTEST_TMP" = "" ] ; then
5 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
66 AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
7 trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
7 trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
88 fi
99
10 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
10 cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
1111
12 cd $AUTOPKGTEST_TMP
13 find . -name "*.gz" -exec gunzip \{\} \;
12 cd "${AUTOPKGTEST_TMP}"
13 gunzip -r *
1414
15 echo "g3-from-scratch"
16 echo "##################################"
17 tigr-glimmer long-orfs -n -t 1.15 example.fa run1.longorfs
18 tigr-glimmer extract -t example.fa run1.longorfs > run1.train
19 tigr-glimmer build-icm -r run1.icm < run1.train
20 tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run1.icm run1
21 echo "=================================="
15 echo 'Begin Test'
16 /usr/lib/tigr-glimmer/long-orfs -n -t 1.15 example.fa test1.longorfs
17 /usr/lib/tigr-glimmer/extract -t example.fa test1.longorfs > test1.train
18 /usr/lib/tigr-glimmer/build-icm -r test1.icm < test1.train
19 /usr/lib/tigr-glimmer/glimmer3 example.fa test1.icm test1
20 echo '---------------Passed!----------------------------'
2221
23 # for making this test, need fasta file with coords
24 #echo "g3-from-training"
25 #echo "##################################"
26 #tigr-glimmer extract -t example.fa train.coords > run2.train
27 #tigr-glimmer build-icm -r run2.icm < run2.train
28 #tigr-glimmer upstream-coords.awk 25 0 train.coords | extract example.fa - > run2.upstream
29 ##elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
30 ##set startuse = ‘start-codon-distrib -3 example.fa train.coords‘
31 ##tigr-glimmer glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse example.fa run2.icm run2
32
33 echo "g3-iterated"
34 echo "##################################"
35 tigr-glimmer long-orfs -n -t 1.15 example.fa run3.longorfs
36 tigr-glimmer extract -t example.fa run3.longorfs > run3.train
37 tigr-glimmer build-icm -r run3.icm < run3.train
38 tigr-glimmer glimmer3 -o50 -g110 -t30 example.fa run3.icm run3.run1
39 tail -n+2 run3.run1.predict > run3.coords
40 # for making full test, need elph (elph not in repo)
41 #upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
42 #elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
43 #set startuse = ‘start-codon-distrib -3 genom.seq run3.coords‘
44 #tigr-glimmer glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
45 echo "=================================="
46
47 echo "PASS"