Package list tigr-glimmer / 089e7d8
Autopkgtest added cbk-guest 5 years ago
5 changed file(s) with 99 addition(s) and 1 deletion(s). Raw diff Collapse all Expand all
00 tigr-glimmer (3.02-5) UNRELEASED; urgency=medium
11
2 [ Andreas Tille ]
23 * Moved packaging from SVN to Git
34
4 -- Andreas Tille <tille@debian.org> Thu, 11 Aug 2016 20:28:02 +0200
5 [ Canberk Koç ]
6 * Autopkgtest added
7
8 -- Canberk Koç <canberkkoc@gmail.com> Fri, 12 Aug 2016 07:29:52 +0300
59
610 tigr-glimmer (3.02-4) unstable; urgency=medium
711
0 Tests: run-unit-test
1 Depends: @
2 Restrictions: allow-stderr
0 #!/bin/bash
1 set -e
2
3 pkg="tigr-glimmer"
4
5 if [ "$AUTOPKGTEST_TMP" = "" ] ; then
6 AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
7 trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
8 fi
9
10 cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
11
12 cd $AUTOPKGTEST_TMP
13 find . -name "*.gz" -exec gunzip \{\} \;
14
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 "=================================="
22
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"
0 >CALM_HUMAN
1 MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDAD
2 GNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLT
3 DEEVDEMIREADIDGDGQVNYEEFVQMMTAK
4 >AF01595 Human telomerase reverse transcriptase (hTRT) mRNA
5 MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRALVAQCLVCVP
6 WDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTTS
7 VRSYLPNTVTDALRGSGAWGLLLRRVGDDVLVHLLARCALFVLVAPSCAYQVCGPPLYQ
8 LGAATQARPPPHASGPRRRLGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLPLPK
9 RPRRGAAPEPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGTRHS
10 HPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRPSFLLSSLRPSL
11 TGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKTHC
12 PLRAAVTPAAGVCAREKPQGSVAAPEEEDTDPRRLVQLLRQHSSPWQVYGFVRACLRRL
13 VPPGLWGSRHNERRFLRNTKKFISLGKHAKLSLQELTWKMSVRDCAWLRRSPGVGCVPA
14 AEHRLREEILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSIGIR
15 QHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMDYVVGARTFRREK
16 RAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDIHRAWRTFVLRVRAQDPPPELYF
17 VKVDVTGAYDTIPQDRLTEVIASIIKPQNTYCVRRYAVVQKAAHGHVRKAFKSHVSTLT
18 DLQPYMRQFVAHLQETSPLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKSYV
19 QCQGIPQGSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKTFLR
20 TLVRGVPEYGCVVNLRKTVVNFPVEDEALGGTAFVQMPAHGLFPWCGLLLDTRTLEVQS
21 DYSSYARTSIRASLTFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYK
22 ILLLQAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAA
23 GPLPSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANP
24 ALPSDFKTILD
25 >P53_HUMAN
26 MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
27 DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK
28 SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE
29 RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS
30 SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGRDRRTEEENLRKKGEPHHELP
31 PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG
32 GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
33 >TUBE_DROME
34 MAYGWNGCGMGVQVNGSNGAIGLSSKYSRNTELRRVEDNDIYRLAKILDENSCWRKLMS
35 IIPKGMDVQACSGAGCLNFPAEIKKGFKYTAQDVFQIDEAANRLPPDQSKSQMMIDEWK
36 TSGKLNERPTVGVLLQLLVQAELFSAADFVALDFLNESTPARPVDGPGALISLELLEEE
37 MEVDNEGLSLKYQSSTATLGADAQGSVGLNLDNFEKDIVRRDKSVPQPSGNTPPIAPPR
38 RQQRSTTNSNFATLTGTGTTSTTIPNVPNLTILNPSEQIQEPVLQPRPMNIPDLSILIS
39 NSGDLRATVSDNPSNRTSSTDPPNIPRITLLIDNSGDVNSRPNHAPAKASTATTPTASS
40 NNLPMISALNISKGSKETLRPESRSSSSSLSKDDDDDNDGEEDGEEEYPDAFLPNLSNS
41 EQQSSNNDSSLTTVTGTSGDNSFELTNDSSSTSNDDYACNIPDLSELQQ
0 debian/tests.tigr-glimmer/*