Pranav Ballaney pushed to branch master at Debian Med / kalign
Commits: 79ce77e9 by Pranav Ballaney at 2020-03-21T01:13:38+05:30 Reinstall examples properly - - - - - aed13991 by Pranav Ballaney at 2020-03-21T01:13:42+05:30 Add more autopkgtests - - - - - 4 changed files: - debian/kalign.examples - − debian/tests/data/BB11001.msf - − debian/tests/data/BB11001.tfa - debian/tests/run-unit-test Changes: ===================================== debian/kalign.examples ===================================== @@ -1 +1,2 @@ -debian/tests/data/* \ No newline at end of file +debian/tests/data/* +dev/data/B* \ No newline at end of file ===================================== debian/tests/data/BB11001.msf deleted ===================================== @@ -1,26 +0,0 @@ -PileUp - - - - MSF: 96 Type: P Check: 7038 .. - - Name: 1aab_ oo Len: 96 Check: 4681 Weight: 10.0 - Name: 1j46_A oo Len: 96 Check: 1914 Weight: 10.0 - Name: 1k99_A oo Len: 96 Check: 8221 Weight: 10.0 - Name: 2lef_A oo Len: 96 Check: 2222 Weight: 10.0 - -// - - - -1aab_ ...GKGDPKK PRGKMSSYAF FVQTSREEHK KKHPDASVNF SEFSKKCSER -1j46_A ......MQDR VKRPMNAFIV WSRDQRRKMA LENP..RMRN SEISKQLGYQ -1k99_A MKKLKKHPDF PKKPLTPYFR FFMEKRAKYA KLHP..EMSN LDLTKILSKK -2lef_A ........MH IKKPLNAFML YMKEMRANVV AEST..LKES AAINQILGRR - - -1aab_ WKTMSAKEKG KFEDMAKADK ARYEREMKTY IPPKGE.... ...... -1j46_A WKMLTEAEKW PFFQEAQKLQ AMHREKYPNY KYRPRRKAKM LPK... -1k99_A YKELPEKKKM KYIQDFQREK QEFERNLARF REDHPDLIQN AKK... -2lef_A WHALSREEQA KYYELARKER QLHMQLYPGW SARDNYGKKK KRKREK - ===================================== debian/tests/data/BB11001.tfa deleted ===================================== @@ -1,12 +0,0 @@ ->1aab_ -GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT -MSAKEKGKFEDMAKADKARYEREMKTYIPPKGE ->1j46_A -MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAE -KWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK ->1k99_A -MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYK -ELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK ->2lef_A -MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQA -KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK \ No newline at end of file ===================================== debian/tests/run-unit-test ===================================== @@ -14,6 +14,8 @@ cd $AUTOPKGTEST_TMP gunzip -r * +ls + # Passing input files via -i never works for some reason inside the testing chroot # LOG : kalign -i BB11001.tfa -f msf -o out.msf # ERROR : Input alignment format could not be detected. (rwalign.c line 314) @@ -37,17 +39,25 @@ cat seqsA.fa seqsB.fa seqsC.fa | kalign -f fasta > combined.afa echo TEST 4: Align sequences and output the alignment in MSF format # kalign -i BB11001.tfa -f msf -o out.msf cat BB11001.tfa | kalign -f msf -o out.msf +cat BB12006.tfa | kalign -f msf -o out.msf +cat BB30014.tfa | kalign -f msf -o out.msf echo TEST 5: Align sequences and output the alignment in clustal format # kalign -i BB11001.tfa -f clu -o out.clu cat BB11001.tfa | kalign -f clu -o out.clu +cat BB12006.tfa | kalign -f clu -o out.clu +cat BB30014.tfa | kalign -f clu -o out.clu echo TEST 6: Re-align sequences in an existing alignment # kalign -i BB11001.msf -o out.afa cat BB11001.msf | kalign -o out.afa +cat BB12006.msf | kalign -o out.afa +cat BB30014.msf | kalign -o out.afa echo TEST 7: Reformat existing alignment # kalign -i BB11001.msf -r afa -o out.afa cat BB11001.msf | kalign -r afa -o out.afa +cat BB12006.msf | kalign -r afa -o out.afa +cat BB30014.msf | kalign -r afa -o out.afa echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/fa43b96ec7d1ba23d7a401562f375f5d057ab25b...aed1399182de322bcfb255e946ef845390188a79 -- View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/fa43b96ec7d1ba23d7a401562f375f5d057ab25b...aed1399182de322bcfb255e946ef845390188a79 You're receiving this email because of your account on salsa.debian.org.
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