Autopkgtest added
cbk-guest
7 years ago
| 0 | 0 | tigr-glimmer (3.02-5) UNRELEASED; urgency=medium |
| 1 | 1 | |
| 2 | [ Andreas Tille ] | |
| 2 | 3 | * Moved packaging from SVN to Git |
| 3 | 4 | |
| 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 | |
| 5 | 9 | |
| 6 | 10 | tigr-glimmer (3.02-4) unstable; urgency=medium |
| 7 | 11 |
| 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/* |