From 1e7f33d63be100c3124a822c8868c4661bcc5560 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Tue, 20 Nov 2012 16:11:49 +0100
Subject: [PATCH] added unit tests for kclust binding
---
modules/bindings/tests/CMakeLists.txt | 1 +
modules/bindings/tests/test_kclust.py | 44 ++++++++++++++
modules/bindings/tests/testfiles/clusters.dmp | 30 ++++++++++
.../bindings/tests/testfiles/fastadb.fasta | 58 +++++++++++++++++++
modules/bindings/tests/testfiles/headers.dmp | 29 ++++++++++
5 files changed, 162 insertions(+)
create mode 100644 modules/bindings/tests/test_kclust.py
create mode 100644 modules/bindings/tests/testfiles/clusters.dmp
create mode 100644 modules/bindings/tests/testfiles/fastadb.fasta
create mode 100644 modules/bindings/tests/testfiles/headers.dmp
diff --git a/modules/bindings/tests/CMakeLists.txt b/modules/bindings/tests/CMakeLists.txt
index d1b344ff5..7b04104d9 100644
--- a/modules/bindings/tests/CMakeLists.txt
+++ b/modules/bindings/tests/CMakeLists.txt
@@ -2,6 +2,7 @@ set(OST_BINDINGS_UNIT_TESTS
test_msms.py
test_clustalw.py
test_blast.py
+ test_kclust.py
)
ost_unittest(MODULE bindings
diff --git a/modules/bindings/tests/test_kclust.py b/modules/bindings/tests/test_kclust.py
new file mode 100644
index 000000000..fe7251613
--- /dev/null
+++ b/modules/bindings/tests/test_kclust.py
@@ -0,0 +1,44 @@
+import sys
+import unittest
+from ost import *
+from ost import settings
+from ost.bindings import kclust
+
+class TestkClustBindings(unittest.TestCase):
+
+ def testkClustExec(self):
+
+ seq_list=io.LoadSequenceList('testfiles/multiple.fasta')
+
+ clusters40=kclust.kClust(seq_list,clustering_thresh=40)
+ clusters90=kclust.kClust(seq_list,clustering_thresh=90)
+
+ self.assertEqual(len(clusters40),16)
+ self.assertEqual(len(clusters90),27)
+
+ def testkClustParseOutput(self):
+
+ representative_ids=['Q5KTS5.1','P46331.2','P66776.1','P42317.2','P50199.1',
+ 'Q59787.1','Q9WYG0.1','P50197.1','P50198.1','Q7Z4W1.2',
+ 'Q04520.1']
+
+ cluster_sizes=[3,3,4,1,7,3,2,1,1,3,1]
+
+ result=kclust._ParseOutput('testfiles')
+
+ self.assertEqual(len(result),11)
+
+ for c, r_id in zip(result, representative_ids):
+ self.assertEqual(c.representative_id, r_id)
+ for c, s in zip(result, cluster_sizes):
+ self.assertEqual(len(c.sequences),s)
+
+if __name__ == "__main__":
+ # test if kClust is available on system, otherwise ignore tests
+ try:
+ blastpath=settings.Locate(('kClust'))
+ except(settings.FileNotFound):
+ print "Could not find kClust executable: ignoring unit tests"
+ sys.exit(0)
+ from ost import testutils
+ testutils.RunTests()
diff --git a/modules/bindings/tests/testfiles/clusters.dmp b/modules/bindings/tests/testfiles/clusters.dmp
new file mode 100644
index 000000000..f3974d214
--- /dev/null
+++ b/modules/bindings/tests/testfiles/clusters.dmp
@@ -0,0 +1,30 @@
+# 29
+1 1
+2 1
+3 1
+4 4
+17 4
+18 4
+5 5
+6 5
+7 5
+10 5
+8 8
+9 9
+13 9
+14 9
+15 9
+16 9
+23 9
+25 9
+11 11
+12 11
+24 11
+19 19
+22 19
+20 20
+21 21
+26 26
+27 26
+28 26
+29 29
diff --git a/modules/bindings/tests/testfiles/fastadb.fasta b/modules/bindings/tests/testfiles/fastadb.fasta
new file mode 100644
index 000000000..56895f504
--- /dev/null
+++ b/modules/bindings/tests/testfiles/fastadb.fasta
@@ -0,0 +1,58 @@
+>P50198.1
+MANRLAGKVALITGGASGLGAAQAKRFAEEGAKVVIGDLNEEMAKGVVAEIRAAGGDALFIRLDVTDAASWNNAIAAAVDGFGGLTTLSNTAGIIHPGGFEEESIEGWNKMVAVNQTAIFLGIKAAIPELVKSGNGSIINISSLIGMFPTAGNASYCATKAAVRIMSKAAALEFVDRGVRVNTIVPGGMNTPITANVPPDVLKQQTSQIPMGKLGDPIDIANGALFLASDEAKYITGVDLPIDGGWSVGV
+>Q9WYG0.1
+MNFQGKVVLITGAGSGIGKKAAVMFAERGAKVAINDISEEKGKETVELIKSMGGEAAFIFGDVAKDAEQIVKKTVETFGRLDILVNNAGIVPYGNIEETSEEDFDKTMAVNVKGPFLLSKYAVEQMKKQGGGVIVNVSSEAGLIGIPRRCVYSVSKAALLGLTRSLAVDYVDYGIRVNAVCPGTTQSEGLMARVKASPNPEELLKKMTSRIPMKRLGKEEEIAFAILFAACDEAGFMTGSIINIDGGSTAV
+>Q8KWT4.1
+MNLTDKTVLITGGASGIGYAAVQAFLNQQANVVVADIDEAQGEAMIRKENNDRLHFVHTDITDEPACQNAIRSAVDKFGGLDVLINNAGIEIVAPIHEMELSNWNKVLNVNLTGMFLMSKHALKYMLKSGKGNIINTCSVGGVVAWPDIPAYNASKGGVLQLTRSMAVDYAKHNIRVNCVCPGIIDTPLNEKSFLENNEGTLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ
+>P39640.2
+MNLTDKTVLITGGASGIGYAAVQAFLGQQANVVVADIDEAQGEAMVRKENNDRLHFVQTDITDEAACQHAVESAVHTFGGLDVLINNAGIEIVAPIHEMELSDWNKVLQVNLTGMFLMSKHALKHMLAAGKGNIINTCSVGGLVAWPDIPAYNASKGGVLQLTKSMAVDYAKHQIRVNCVCPGIIDTPLNEKSFLENNEGTLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ
+>P46331.2
+MGRLENKTAVITGAATGIGQATAEVFANEGARVIIGDINKDQMEETVDAIRKNGGQAESFHLDVSDENSVKAFADQIKDACGTIDILFNNAGVDQEGGKVHEYPVDLFDRIIAVDLRGTFLCSKYLIPLMLENGGSIINTSSMSGRAADLDRSGYNAAKGGITNLTKAMAIDYARNGIRVNSISPGTIETPLIDKLAGTKEQEMGEQFREANKWITPLGRLGQPKEMATVALFLASDDSSYVTGEDITADGGIMAYTWPGKMLIEEKWKEETK
+>P50197.1
+MSDLSGKTIIVTGGGSGIGRATVELLVASGANVPVADINDEAGEAVVATSGGKAAYFRCDIAQEEDVKALVAQTLAAFGGLDGSFNNAAIPQAGLPLAEVSLERFRQSMDINVTGTFLCMKYQILAMIERGTKGSIVNTASAAGVVGVPMHGEYVGAKHAVVGLTRVAAADYGKHGIRVNALVPGAVRTPMLQRAMDNDAGLEPYLNSIHPIGRFSEPHEQAQAAVWLLSDAASFVTGSCLAADGGFTAI
+>P42317.2
+MRKQVALVTGAAGGIGFEIAREFAREGASVIVSDLRPEACEKAASKLAEEGFDAAAIPYDVTKEAQVADTVNVIQKQYGRLDILVNNAGIQHVAPIEEFPTDTFEQLIKVMLTAPFIAMKHVFPIMKKQQFGRIINIASVNGLVGFAGKSAYNSAKHGVIGLTKVGALEGAPHGITVNALCPGYVDTQLVRNQLSDLSKTRNVPYDSVLEQVIFPLVPQKRLLSVKEIADYAVFLASEKAKGVTGQAVVLDGGYTAQ
+>target
+MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS
+>Q59787.1
+MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS
+>Q48436.2
+MKKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATAKAVASEINQAGGRAMAVKVDVSDRDQVFAAVEQARKTLGGFDVIVNNAGVAPSTPIESITPEIVDKVYNINVKGVIWGIQAAVEAFKKEGHGGKIINACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGYCPGIVKTPMWAEIDRQVSEAAGKPLGYGTAEFAKRITLGRLSEPEDVAACVSYLASPDSDYMTGQSLLIDGGMVFN
+>Q04520.1
+MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGGRAVAIKVDVSRRDQVFAAVEQARKALGGFNVIVNNAGIAPSTPIESITEEIVDRVYNINVKGVIWGMQAAVEAFKKEGHGGKIVNACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRKRRANRWATARLNLPNASPLAACRSLKTSPPACRSSPARIPTI
+>P66776.1
+MTNNKVALVTGGAQGIGFKIAERLVEDGFKVAVVDFNEEGAKAAALKLSSDGTKAIAIKADVSNRDDVFNAVRQTAAQFGDFHVMVNNAGLGPTTPIDTITEEQFKTVYGVNVAGVLWGIQAAHEQFKKFNHGGKIINATSQAGVEGNPGLSLYCSTKFAVRGLTQVAAQDLASEGITVNAFAPGIVQTPMMESIAVATAEEAGKPEAWGWEQFTSQIALGRVSQPEDVSNVVSFLAGKDSDYITGQTIIVDGGMRFR
+>Q5HKG6.1
+MSKTAIITGSAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGYQAVAFKSDVSKKKEQEELVQFAVTEFGQLDVMVNNAGVDAVTPILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR
+>Q8CQD2.1
+MSKTAIITGAAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGYQAVAYKSDVSKKKEQEELVQFAVTEFGQLDVMVNNAGVDAVTPILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRGKIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTERLVADEEFTDWLCKRTPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL
+>P0A9Q0.1
+MNDLFSLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQAVAAPFNVTHKHEIDAAVEHIEKDIGPIDVLVNNAGIQRRHPFTEFPEQEWNDVIAVNQTAVFLVSQAVTRHMVERKAGKVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHNIQVNGIAPGYFKTEMTKALVEDEAFTAWLCKRTPAARWGDPQELIGAAVFLSSKASDFVNGHLLFVDGGMLVAV
+>Q05528.1
+MILNTFNLQGKVALITGCDTGLGQGMAVGLAEAGCDIVGVNIVEPKETIEKVTAVGRRFLSLTADMSDISGHAALVEKAVAEFGKVDILVNNAGIIRREDAIEFSEKNWDDVMNLNIKSVFFMSQTVARQFIKQGHGGKIINIASMLSFQGGIPVPSYTASKKRVMGITRIVANEWAKHNINVNAIAPGYMATNNTQHVRADQDRSKEILDRIPAGRWGLPQDLQGPAVFLASSASDYVNGYTIAVDGGWLAR
+>P37769.2
+MILSAFSLEGKVAVVTGCDTGLGQGMALGLAQAGCDIVGINIVEPTETIEQVTALGRRFLSLTADLRKIDGIPALLDRAVAEFGHIDILVNNAGLIRREDALEFSEKDWDDVMNLNIKSVFFMSQAAAKHFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWAKHNINVNAIAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPIVFLASSASDYVNGYTIAVDGGWLAR
+>P50842.1
+MGYLHDAFSLKGKTALVTGPGTGIGQGIAKALAGAGADIIGTSHTSSLSETQQLVEQEGRIFTSFTLDMSKPEAIKDSAAELFENRQIDILVNNAGIIHREKAEDFPEENWQHVLNVNLNSLFILTQLAGRHMLKRGHGKIINIASLLSFQGGILVPAYTASKHAVAGLTKSFANEWAASGIQVNAIAPGYISTANTKPIRDDEKRNEDILKRIPAGRWGQADDIGGTAVFLASRASDYVNGHILAVDGGWLSR
+>Q1JP75.1
+MDLRLAGRRALVTGAGKGIGRSIVKALHAAGARVVAVSRTQADLDSLVRECPGVETVCVDLADWEATEQALGGVGPVDLLVNNAAVAFLQPFLEVTKEAYDMSFSVNLRAVIQVSQIVARGLIARGAPGVIVNVSSQASQRGLTNHSVYCSTKGALDTLTKVMAVELGPHKIRVNAVNPTVVMTPMGQAAWSDPQKAKAMLDRIPLGRFAEVENVVDTILFLLSDRSSMTTGSTVPVDGGFLAT
+>Q91XV4.1
+MDLGLAGRRALVTGAGKGIGRSTVLALQAAGAHVVAVSRTQADLDSLVSECPGVETVCVDLADWEATEQALSSVGPVDLLVNNAAVALLQPFLEVTKEAFDMSFNVNLRAVIQVSQIVARGMIARGAPGAIVNVSSQASQRALANHSVYCSTKGALDMLTKMMALELGPHKIRVNAVNPTVVMTSMGRTNWSDPHKAKVMLDRIPLGKFAEVENVVDAILFLLSHRSNMTTGSTLPVDGGFLVT
+>Q7Z4W1.2
+MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECPGIEPVCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHKAKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC
+>P40397.2
+MANQKKKTLPPQHQNQQPGFEYLMDPRPVFDKPKKAKKLEGKTAIITGGDSGIGRAVSVLFAKEGANVVIVYLNEHQDAEETKQYVEKEGVKCLLIAGDVGDEAFCNDVVGQASQVFPSIDILVNNAAEQHVQPSIEKITSHQLIRTFQTNIFSMFYLTKAVLPHLKKGSSIINTASITAYKGNKTLIDYSATKGAIVTFTRSLSQSLVQQGIRVNAVAPGPIWTPLIPASFAAKDVEVFGSDVPMERPGQPVEVAPSYLYLASDDSTYVTGQTIHVNGGTIVNG
+>O07575.1
+MNPMDRQTEGQEPQHQDRQPGIESKMNPLPLSEDEDYRGSGKLKGKVAIITGGDSGIGRAAAIAFAKEGADISILYLDEHSDAEETRKRIEKENVRCLLIPGDVGDENHCEQAVQQTVDHFGKLDILVNNAAEQHPQDSILNISTEQLEKTFRTNIFSMFHMTKKALPHLQEGCAIINTTSITAYEGDTALIDYSSTKGAIVSFTRSMAKSLADKGIRVNAVAPGPIWTPLIPATFPEEKVKQHGLDTPMGRPGQPVEHAGAYVLLASDESSYMTGQTIHVNGGRFIST
+>Q5KTS5.1
+MASGGQFPPQKQESQPGKEHLMDPSPQHASPHYKPANKLQGKVALVTGGDSGIGRSVCYHFALEGATVAFTFVKGHEDKDANETLELLRKAKSSDAKDPIAIAADLGFDDNCKKVVDQVVNAFGSIDVLVNNAAEQYKASTVEDIDEERLERVFRTNIFAYFFMARHALKHMREGSTIINTTSINAYKGNAKLLDYTATKGAIVAFTRGLSLQLISKGIRVNGVAPGPVWTPLIPSSFDEEEVKQFGSEVPMKRAGQPYEIATAYVFLASCDSSYYSGQVLHPNGGAIVNG
+>Q49117.2
+MSKLEGKVAVVTGASKGIGAAIAKALAKDGAAVVVNYASSKAGADAVVEAITAAGGKAIAVQADVSQAVQARGLVEAAVQQFGRLDVLVNNSGVYEFAAIEEVTEEHYRRIFDVNVLGVLLATQAASKHLGEGGSIINISSVVTDVLMPTSAVYSGTKGALNAISGVLANELAPRKIRVNVVSPGYVVTEGTHTAGIAGSEMEAGLVAQTPLGRSGQPDDIAGVVAFLASDDARWVTGEVINASGGVR
+>Q9KQH7.2
+MNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNGKGMALNVTNPESIEAVLKAITDEFGGVDILVNNAGITRDNLLMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQGRIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQRTATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI
+>P55336.1
+MNLEGKIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKTINDECGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRGMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDDQRAATLSNVPAGRLGDPREIASAVVFLASPEAAYITGETLHVNGGMYMV
+>P0A2C9.1
+MSFEGKIALVTGASRGIGRAIAETLVARGAKVIGTATSENGAKNISDYLGANGKGLMLNVTDPASIESVLENIRAEFGEVDILVNNAGITRDNLLMRMKDDEWNDIIETNLSSVFRLSKAVMRAMMKKRCGRIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGFIETDMTRALSDDQRAGILAQVPAGRLGGAQEIASAVAFLASDEASYITGETLHVNGGMYMV
diff --git a/modules/bindings/tests/testfiles/headers.dmp b/modules/bindings/tests/testfiles/headers.dmp
new file mode 100644
index 000000000..7c188177f
--- /dev/null
+++ b/modules/bindings/tests/testfiles/headers.dmp
@@ -0,0 +1,29 @@
+1 >Q5KTS5.1
+2 >O07575.1
+3 >P40397.2
+4 >P46331.2
+17 >P39640.2
+18 >Q8KWT4.1
+5 >P66776.1
+6 >Q8CQD2.1
+7 >Q5HKG6.1
+10 >Q48436.2
+8 >P42317.2
+9 >P50199.1
+13 >P50842.1
+14 >P0A9Q0.1
+15 >P37769.2
+16 >Q05528.1
+23 >P0A2C9.1
+25 >Q9KQH7.2
+11 >Q59787.1
+12 >target
+24 >P55336.1
+19 >Q9WYG0.1
+22 >Q49117.2
+20 >P50197.1
+21 >P50198.1
+26 >Q7Z4W1.2
+27 >Q91XV4.1
+28 >Q1JP75.1
+29 >Q04520.1
--
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