[med-svn] [Git][med-team/kalign][master] 2 commits: Reinstall examples properly

[Pranav Ballaney]

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
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