[med-svn] [Git][med-team/kalign][master] 2 commits: Install more test files
Pranav Ballaney
gitlab at salsa.debian.org
Thu Mar 19 19:47:27 GMT 2020
Pranav Ballaney pushed to branch master at Debian Med / kalign
Commits:
f9e2c501 by Pranav Ballaney at 2020-03-20T00:56:25+05:30
Install more test files
- - - - -
fa43b96e by Pranav Ballaney at 2020-03-20T01:15:59+05:30
Add autopkgtests
- - - - -
8 changed files:
- debian/kalign.examples
- + debian/tests/data/BB11001.msf
- + debian/tests/data/BB11001.tfa
- debian/tests.kalign/example.fa → debian/tests/data/example.fa
- + debian/tests/data/seqsA.fa
- + debian/tests/data/seqsB.fa
- + debian/tests/data/seqsC.fa
- debian/tests/run-unit-test
Changes:
=====================================
debian/kalign.examples
=====================================
@@ -1 +1 @@
-debian/tests.kalign/*
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/tests/data/BB11001.msf
=====================================
@@ -0,0 +1,26 @@
+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
=====================================
@@ -0,0 +1,12 @@
+>1aab_
+GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT
+MSAKEKGKFEDMAKADKARYEREMKTYIPPKGE
+>1j46_A
+MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAE
+KWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK
+>1k99_A
+MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYK
+ELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK
+>2lef_A
+MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQA
+KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK
\ No newline at end of file
=====================================
debian/tests.kalign/example.fa → debian/tests/data/example.fa
=====================================
=====================================
debian/tests/data/seqsA.fa
=====================================
@@ -0,0 +1,20 @@
+>random sequence 1 consisting of 500 residues
+QWKPFLTTAQSKLFEMIQHAEMDCPASDYKYPAHESVRVSYCFGCFGHQSTLFAQCQAKL
+SNIESSIEGYAFPSVYWYNNHKHPTNNDHIGPACAVTQGKCDYNPANPFSWLVNIPEYQG
+TFVPNTNLNWKIGNIMGWFYTVVMADYCDQWYEDVFTISWCPRAFKLEDRWDRVTDANTK
+PSKLWFNNRQEPAYQWMDSPDHKVRRIVLTPRNMFTETKSCYAVETRNCDGLHVVVHETM
+TAKREDNIGEWHILKTHQNKGWVKQKMHAEMSALEFDAYLLVGMARMQCRVYQHNAKIRN
+TDSPVVFCKWYGTATHKQPSSCMCEDEVSDGKMWYGWNHYQYLAEFDDGAPHHLECTWAM
+DYNPDAAQPMPYDCNNCAFQNQVHFTIDRGFQHGTRNQVHNRVDQDENYMGISEFTNYFL
+DQCDFIQEQIDSDTESNHQCYTWAKLTRYVQVTNPRSDMGAVIENREMENCVEQGAHSDN
+HSPVNMEKWYCECESPPKNV
+>random sequence 2 consisting of 500 residues
+PDGNKPKEPWKGPKMGQDMVTNSIVNTPGDDTKGFDEMIWLMDKRTRLVVKACMWPMILA
+LNTYQNKNDNEMPWPHWGMRMHGHDLLQRRKPIFQQYTIVAMFNMGSSDQQEFLMIKPPI
+QATCSSGLDPHRLMRCYKWDTKKTQKGDHKGQEKCQSEAVYDKCIIKQVVFHSMYCYWTY
+WCICYLPTAEMGDDYQPECWHVWYIMDYVVKFKMLYNNRLWYSHMNQMWINHHIHVYYRC
+GDQYLADHPYRMGIVDAYWFISFGHRIRQRMCVQLKVWGWVFLNAAGSPVHRFKSAHHVG
+GGADGRMPRTCRDDPRMYEAKWSYAPPYVITCALRPGMFANYHPRSFVRPCQQPMYWMRN
+MLSDQSEAYGGNVDMGWLARDNISSQCYHSDIQWPGIQMILHSPAANPGHHQIACVKRSH
+TEALELFQAVTASNVAIGCFIQTACPIDMSIEKPDDAIMEWPGYTFGYDRTRCKWTRAND
+IPHPDKNKSSGLRCYHTVNL
\ No newline at end of file
=====================================
debian/tests/data/seqsB.fa
=====================================
@@ -0,0 +1,20 @@
+>random sequence 3 consisting of 500 residues
+PTANCDANENICAHSYFKLLMIFDFWYDYFVLCRATIHHMHYWRPCFEPPYHIVWKYKDM
+HRCLANYWTHQMKTVSVRRINNNEARWMIREWHGSSWGIMLMVKKLVTTQWHPYNFREEE
+PWYMNIPPWEVGQEIKAFVCLECAGPEMWPNCQDKNSPYMTGSLLVGGDVRYTIMQWDLE
+APKIKRETPGESWAPLLIFCRMKAMQQDGVAGLEKTGGHLMQCRHLGHAVHRRHNNMHTC
+LCSYVDQWCSHMKWSWWDHRFERNLMKYPIIMIAFCPFVRDHCPLWAIMQKGTSHEVQHR
+YVQCQVFPYNEMIHSPCMPYLSCHQRLKLHDGEYKTHTGLIYDMEAKCQLSEAMRHTSMR
+ESACGQHYNYAKQSDHRFKLDAFTHYDFDFDRLKSGNCCSTISACICYAKPVAWRMRCMM
+IWTTGKCTKNCFDGCSYICPTIQNTQCLWEMSQYWADLDPKKKFWFWPSATIYWTEGIVQ
+EHSLTIWTLDTGVVIGLADP
+>random sequence 4 consisting of 500 residues
+NQLFCNMDIYHRGVREQKMFHNCESICQKHKAIAVRMANKTPRQSLMMTCSALQHSNPTT
+NEYLQDTKVWYFMQALRVSRSWGWRASYFYRPMDYKRNWHEPVRHPATWCFPIWCFNIPM
+WHGHDYQMHTLRLLSMKCNCYDWRDNFDEYFTDPSAQSKHNHMADYVLLMIQLLKIARYR
+INVWDTHLMWRNLSQQVPYIMHPYSDHLREWTNANFKFIWQQGMCQHEMTYGKIWDVMGG
+EYCTTVMKHHWAVAKHHPALPHQERRIIGLVWKMSNKWAANFGSCNWELYIGLHQQASKG
+PSAWGLMCMCYHTRYHRALQRLSDAHCNWDDDKYHWGKKESAEVNTSDSHFRHCTRWEMV
+NDYVNGSNTHHDAEKRHEAIPCPYHPGYRCFVCGSNDIYVCISCTKKGAWSMHPWMWNGM
+TDRSRVTCTITCMHILQIPTHVDAHPIDTPYQLSFFMIIEMNNVQMRDMPHIMYVMWAGS
+AIALCWWEHHTHNYRTIDWF
\ No newline at end of file
=====================================
debian/tests/data/seqsC.fa
=====================================
@@ -0,0 +1,20 @@
+>random sequence 5 consisting of 500 residues
+RNLELKAMVFEFPHAWAIKHAWLAFLNHGSTLRRMRIFCHHYRALHTSLIFIWISMNWYF
+NIQNMSAMTNDTLCLCGNTTNLQHTGIPAWYDKCNHPRIDDMVEVQDWKERWQHHGHYEG
+VHNIGTMMSKDSFHNKEGKGERWPEWDYRITIMLSYHCEEQHPKCTWKMKAGCMGAVLWD
+MEFCFRGPQNSGPHWCQMEQYLGPNGRNMGEDINHMAFNTHWDITLQDLTDAPYREPHDK
+QYACLPMKPHIPFMFVGDADSDFGWDQPDTDGNMMRPLHPWGEIQIHKCNCFCHPCDQEV
+MNWLLCMWEEVPDWLTNKGARTNARCPYGHPICMIEERNALPSSQHKIVLTSLKWMNRIE
+DDGMGLNYNYQCDASLWCGVIRWPYIHHWEETGCLDYGQTKELRYCMIRFFGKRIDHNSL
+SLGKDIACAQQHTHMWTSAVPCARHEVDQATLKHCDAFPRGPQTSYQMKLYRCSNPETYW
+PRQCHQSVIQNLMRNKWDST
+>random sequence 6 consisting of 500 residues
+RKPARRCVCSKNMNHYDNEQCGWEQPWLEISFMMSWGVHPEANHIKPVEGLSWVEHVSEF
+IIRYYDWSNSSFQHYKPEVEWMPSAREDEHFKETRQPTPNAYNIGERWKWSYWLGNEKEY
+SNWQMTCDYLDFQKIQDMPRSGPGQLCGSPLYMEISPIWWKGLGCVAHLWMKFPWKIQHI
+SACHHSTGDDQMKTGSDDDGAEDNAINIGKTWQGYDKERCTWLHIMMTGYIRWCCSKDRM
+PSKPFIHNHYIILRKSMWLTDKSKDGDCWVLIANSRGDPCAGNAAHIYPKQMCHRPSLQV
+FEWMFCCPLHDRQGWLKDWNSRSNGTSPKPTLRAEKMFMFHTFLPCFPVHYLMHTRMDHM
+FMMMTTEDKSDKKKDDAEGRMILDYRCKRCPIVCWGVNDHKYSHGHHDMNGAEAEKYYKM
+DMSALRTFPGCCSDNESDGNDRGYDDQGLKRFIFFCKQKAYYICYCRVRSMWHVSRKHNC
+MNTKQCEMESIWGFIIFNSN
\ No newline at end of file
=====================================
debian/tests/run-unit-test
=====================================
@@ -12,11 +12,42 @@ cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
cd $AUTOPKGTEST_TMP
-echo "---test1---"
-/usr/bin/kalign < example.fa > output1
-cat output1
-echo "---test2---"
-/usr/bin/kalign -gpo 60 -gpe 9 -tgpe 0 -bonus 0 < example.fa > output2
-cat output2
+gunzip -r *
+
+# 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)
+# ERROR : Function "detect_alignment_format(b, &type)" failed. (rwalign.c line 187)
+# ERROR : Function "tmp_msa = read_input(param->infile[i],tmp_msa)" failed. (run_kalign.c line 383)
+# ERROR : Function "run_kalign(param)" failed. (run_kalign.c line 353)
+
+# However, input through stdin works
+# Input via -i also works outside the chroot, just not inside it
+
+echo TEST 1: Passing sequences via stdin
+cat example.fa | kalign -f fasta > out.afa
+
+# echo TEST 2: Passing sequences via flags
+# kalign -f fasta -i example.fa -o out.afa
+
+echo TEST 3: Combining multiple input files
+# kalign -i seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa
+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
+
+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
+
+echo TEST 6: Re-align sequences in an existing alignment
+# kalign -i BB11001.msf -o out.afa
+cat BB11001.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
echo "PASS"
View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b
--
View it on GitLab: https://salsa.debian.org/med-team/kalign/-/compare/379ed19b0a9ac4c94c3c00feeb8270260a4e0de2...fa43b96ec7d1ba23d7a401562f375f5d057ab25b
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