modified clustalw bindings and added test case

git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2687 5a81b35b-ba03-0410-adc8-b2c5c5119f08

modules/bindings/pymod/clustalw.py

 from ost.bindings import utils
-from ost import settings, io, seq
+from ost import settings, io, seq, LogError
 import os
 import subprocess
 
-def ClustalW(seq1, seq2, clustalw=None):
+def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False):
   clustalw_path=settings.Locate(('clustalw', 'clustalw2'), 
                                 explicit_file_name=clustalw)
-  seq_list=seq.CreateSequenceList()
-  seq_list.AddSequence(seq1)
-  seq_list.AddSequence(seq2)  
+  
+  if seq2!=None:
+    if isinstance(seq1, seq.SequenceHandle) and isinstance(seq2, seq.SequenceHandle):
+      seq_list=seq.CreateSequenceList()
+      seq_list.AddSequence(seq1)
+      seq_list.AddSequence(seq2)
+    else:
+      LogError("WARNING: Specify at least two Sequences")
+      return
+  elif isinstance(seq1, seq.SequenceList):
+    seq_list=seq1
+  else:
+    LogError("WARNING: Specify either two SequenceHandles or one SequenceList")
+    return
+  
   temp_dir=utils.TempDirWithFiles((seq_list,))
   out=os.path.join(temp_dir.dirname, 'out.fasta')
   command='%s -infile="%s" -output=fasta -outfile="%s"' % (clustalw_path,
@@ -17,15 +29,17 @@ def ClustalW(seq1, seq2, clustalw=None):
   ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
   ps.stdout.readlines()
   aln=io.LoadAlignment(out)
-  aln.SetSequenceOffset(0,seq1.GetSequenceOffset())
-  aln.SetSequenceOffset(1,seq2.GetSequenceOffset())
-  if seq1.HasAttachedView():
-    aln.AttachView(0,seq1.GetAttachedView().Copy())
-  if seq2.HasAttachedView():
-    aln.AttachView(1,seq2.GetAttachedView().Copy())
+  
 
+  for sequence in seq_list:
+    for seq_num,aln_seq in enumerate(aln.sequences):
+      if aln_seq.GetName()==sequence.GetName():
+        break
+    aln.SetSequenceOffset(seq_num,sequence.GetSequenceOffset())
+    if sequence.HasAttachedView():
+      aln.AttachView(seq_num,sequence.GetAttachedView().Copy())
 
-  #~ temp_dir.Cleanup()
+  if not keep_files:
+    temp_dir.Cleanup()
   
   return aln
-  

modules/bindings/tests/CMakeLists.txt

 set(OST_BINDINGS_UNIT_TESTS
   test_msms.py
+  test_clustalw.py
 )
 
 ost_unittest(bindings "${OST_BINDINGS_UNIT_TESTS}")

modules/bindings/tests/test_clustalw.py

+import unittest
+from ost import *
+from ost import settings
+from ost.bindings import clustalw
+
+class TestClustalWBindings(unittest.TestCase):
+  
+  def setUp(self):
+    self.protein = io.LoadEntity("testfiles/testprotein.pdb").Select("cname=A")
+
+    self.targetseq = io.LoadSequence("testfiles/test.fasta")
+    self.targetseq.AttachView(self.protein)
+    self.templseq = io.LoadSequence("testfiles/similar.fasta")
+    self.multseq = io.LoadSequenceList("testfiles/multiple.fasta")
+    self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.fasta")
+    self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
+    
+  def testPairwiseClustalW(self):
+    aln=clustalw.ClustalW(self.targetseq, self.templseq)
+    assert self.pw_alignment.ToString(80) == aln.ToString(80), \
+           "Pairwise alignment differs from precomputed one"
+  
+  def testAttachedViewClustalW(self):
+    aln=clustalw.ClustalW(self.targetseq, self.templseq)
+    assert aln.FindSequence("testseq").HasAttachedView(), \
+           "Aligned sequence doesn't have an attached view"
+    
+  def testMultipleClustalW(self):
+    aln=clustalw.ClustalW(self.multseq)
+    assert self.mult_alignment.ToString(80) == aln.ToString(80), \
+           "Multiple alignment differs from precomputed one"
+
+
+if __name__ == "__main__":
+  # test if clustalw package is available on system, otherwise ignore tests
+  try:
+    clustalw_path=settings.Locate(('clustalw', 'clustalw2'))
+  except(settings.FileNotFound):
+    print "Could not find clustalw executable: ignoring unit tests"
+    exit(0)
+  try:
+    unittest.main()
+  except Exception, e:
+    print e
\ No newline at end of file

modules/bindings/tests/testfiles/multiple.fasta

+>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

modules/bindings/tests/testfiles/multiple_aln.fasta

+>P50198.1
+--------------------------------------MANRLAGKVALITGGASGLGAAQAKRFAEEGAKVVIGDLNEEMAKGVVAEIRAAGGD-------ALFIRLDVTDAASWNNAIAAAVDGFG--GLTTLSNTAGIIHPGG-FEEESIEGWNKMVAVNQTAIFLGIKAAIPELVKSGN-GSIINISSLIGMFPTAGNASYCATKAAVRIMSKAAALEFVDRGVRVNTIVPG-----GMNTP--ITAN-----VPPDVLKQQTSQIPMGKLGDPIDIANGALFLASDEAKYITGVDLPIDGGWSVGV----------------
+>Q9WYG0.1
+--------------------------------------MN--FQGKVVLITGAGSGIGKKAAVMFAERGAKVAINDISEEKGKETVELIKSMGGE-------AAFIFGDVAKDA--EQIVKKTVETFG--RLDILVNNAGIVPYGN-IEETSEEDFDKTMAVNVKGPFLLSKYAVEQMKKQGG-GVIVNVSSEAGLIGIPRRCVYSVSKAALLGLTRSLAVDYVDYGIRVNAVCPGTTQSEGLMAR--VKASP----NPEELLKKMTSRIPMKRLGKEEEIAFAILFAACDEAGFMTGSIINIDGG-STAV----------------
+>Q8KWT4.1
+--------------------------------------MN--LTDKTVLITGGASGIGYAAVQAFLNQQANVVVADIDEAQGEAMIR--KENNDR-------LHFVHTDITDEPACQNAIRSAVDKFG--GLDVLINNAGIEIVAP-IHEMELSNWNKVLNVNLTGMFLMSKHALKYMLKSGK-GNIINTCSVGGVVAWPDIPAYNASKGGVLQLTRSMAVDYAKHNIRVNCVCPGIIDTPLNEKSFLENNEG----TLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ-----------------
+>P39640.2
+--------------------------------------MN--LTDKTVLITGGASGIGYAAVQAFLGQQANVVVADIDEAQGEAMVR--KENNDR-------LHFVQTDITDEAACQHAVESAVHTFG--GLDVLINNAGIEIVAP-IHEMELSDWNKVLQVNLTGMFLMSKHALKHMLAAGK-GNIINTCSVGGLVAWPDIPAYNASKGGVLQLTKSMAVDYAKHQIRVNCVCPGIIDTPLNEKSFLENNEG----TLEEIKKEKAKVNPLLRLGKPEEIANVMLFLASDLSSYMTGSAITADGGYTAQ-----------------
+>P46331.2
+--------------------------------------MGR-LENKTAVITGAATGIGQATAEVFANEGARVIIGDINKDQMEETVDAIRKNGGQ-------AESFHLDVSDENSVKAFADQIKDACG--TIDILFNNAGVDQEGGKVHEYPVDLFDRIIAVDLRGTFLCSKYLIPLMLENG--GSIINTSSMSGRAADLDRSGYNAAKGGITNLTKAMAIDYARNGIRVNSISPGTIETPLIDKLAGTKEQE----MGEQFREANKWITPLGRLGQPKEMATVALFLASDDSSYVTGEDITADGGIMAYTWPGKMLIEEKWKEETK
+>P50197.1
+--------------------------------------MSD-LSGKTIIVTGGGSGIGRATVELLVASGANVPVADINDEAGEAVVA---TSGGK-------AAYFRCDIAQEEDVKALVAQTLAAFG--GLDGSFNNAAIPQAGLPLAEVSLERFRQSMDINVTGTFLCMKYQILAMIERGTKGSIVNTASAAGVVGVPMHGEYVGAKHAVVGLTRVAAADYGKHGIRVNALVPGAVRTPMLQR--AMDNDA----GLEPYLNS---IHPIGRFSEPHEQAQAAVWLLSDAASFVTGSCLAADGGFTAI-----------------
+>P50199.1
+----------------------------------MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLK-------ASTAVFDVTDQDAVIDGVAAIERDMG--PIDILINNAGIQRRAP-LEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTERLVADEEFT----------DWLCKRTPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL----------------
+>P0A9Q0.1
+----------------------------------MN--DLFSLAGKNILITGSAQGIGFLLATGLGKYGAQIIINDITAERAELAVEKLHQEGIQ-------AVAAPFNVTHKHEIDAAVEHIEKDIG--PIDVLVNNAGIQRRHP-FTEFPEQEWNDVIAVNQTAVFLVSQAVTRHMVERKAG-KVINICSMQSELGRDTITPYAASKGAVKMLTRGMCVELARHNIQVNGIAPGYFKTEMTKALVEDEAFT----------AWLCKRTPAARWGDPQELIGAAVFLSSKASDFVNGHLLFVDGGMLVAV----------------
+>Q05528.1
+-----------------------------------MILNTFNLQGKVALITGCDTGLGQGMAVGLAEAGCDIVGVN-IVE-PKETIEKVTAVGRR-------FLSLTADMSDISGHAALVEKAVAEFG--KVDILVNNAGIIRRED-AIEFSEKNWDDVMNLNIKSVFFMSQTVARQFIKQGHGGKIINIASMLSFQGGIPVPSYTASKKRVMGITRIVANEWAKHNINVNAIAPGYMATNNTQHVRADQDRS----------KEILDRIPAGRWGLPQDLQGPAVFLASSASDYVNGYTIAVDGGWLAR-----------------
+>P37769.2
+-----------------------------------MILSAFSLEGKVAVVTGCDTGLGQGMALGLAQAGCDIVGIN-IVE-PTETIEQVTALGRR-------FLSLTADLRKIDGIPALLDRAVAEFG--HIDILVNNAGLIRRED-ALEFSEKDWDDVMNLNIKSVFFMSQAAAKHFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGVTRLMANEWAKHNINVNAIAPGYMATNNTQQLRADEQRS----------AEILDRIPAGRWGLPSDLMGPIVFLASSASDYVNGYTIAVDGGWLAR-----------------
+>P50842.1
+---------------------------------MGYLHDAFSLKGKTALVTGPGTGIGQGIAKALAGAGADIIGTS-HTSSLSETQQLVEQEGRI-------FTSFTLDMSKPE---AIKDSAAELFENRQIDILVNNAGIIHREK-AEDFPEENWQHVLNVNLNSLFILTQLAGRHMLKRGHG-KIINIASLLSFQGGILVPAYTASKHAVAGLTKSFANEWAASGIQVNAIAPGYISTANTKPIRDDEKRN----------EDILKRIPAGRWGQADDIGGTAVFLASRASDYVNGHILAVDGGWLSR-----------------
+>Q9KQH7.2
+----------------------------------------MNLEGKVALVTGASRGIGKAIAELLAERGAKVIGTATSESGAQAISDYLGDNG----------KGMALNVTNPESIEAVLKAITDEFG--GVDILVNNAGITRDNL-LMRMKEEEWSDIMETNLTSIFRLSKAVLRGMMKKRQG-RIINVGSVVGTMGNAGQANYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDEQR------------TATLAQVPAGRLGDPREIASAVAFLASPEAAYITGETLHVNGGMYMI-----------------
+>P55336.1
+----------------------------------------MNLEGKIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENG----------KGLALNVTDVESIEATLKTINDECG--AIDILVNNAGITRDNL-LMRMKDDEWNDIINTNLTPIYRMSKAVLRGMMKKRAG-RIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREVASRGVTVNTVAPGFIETDMTKALNDDQR------------AATLSNVPAGRLGDPREIASAVVFLASPEAAYITGETLHVNGGMYMV-----------------
+>P0A2C9.1
+----------------------------------------MSFEGKIALVTGASRGIGRAIAETLVARGAKVIGTATSENGAKNISDYLGANG----------KGLMLNVTDPASIESVLENIRAEFG--EVDILVNNAGITRDNL-LMRMKDDEWNDIIETNLSSVFRLSKAVMRAMMKKRCG-RIITIGSVVGTMGNAGQANYAAAKAGLIGFSKSLAREVASRGITVNVVAPGFIETDMTRALSDDQR------------AGILAQVPAGRLGGAQEIASAVAFLASDEASYITGETLHVNGGMYMV-----------------
+>P42317.2
+------------------------------------------MRKQVALVTGAAGGIGFEIAREFAREGASVIVSDLRPEACEKAASKLAEEGFD-------AAAIPYDVTKEAQVADTVNVIQKQYG--RLDILVNNAGIQHVAP-IEEFPTDTFEQLIKVMLTAPFIAMKHVFPIMKKQQFG-RIINIASVNGLVGFAGKSAYNSAKHGVIGLTKVGALEGAPHGITVNALCPGYVDTQLVRNQLSDLSKTRNVPYDSVLEQVIFPLVPQKRLLSVKEIADYAVFLASEKAKGVTGQAVVLDGGYTAQ-----------------
+>P40397.2
+MANQKKKT--LPPQHQNQQPGFEYLMDPRPVFDKP--KKAKKLEGKTAIITGGDSGIGRAVSVLFAKEGANVVIVYLN--EHQDAEETKQYVEKE----GVKCLLIAGDVGDEAFCNDVVGQASQVFP--SIDILVNNAAEQHVQPSIEKITSHQLIRTFQTNIFSMFYLTKAVLPHLKKGSS---IINTASITAYKGNKTLIDYSATKGAIVTFTRSLSQSLVQQGIRVNAVAPGPIWTP--LIPASFAAKD---------VEVFGSDVPMERPGQPVEVAPSYLYLASDDSTYVTGQTIHVNGGTIVNG----------------
+>O07575.1
+MNPMDRQTEGQEPQHQDRQPGIESKMNPLPLSEDEDYRGSGKLKGKVAIITGGDSGIGRAAAIAFAKEGADISILYLD--EHSDAEETRKRIEKE----NVRCLLIPGDVGDENHCEQAVQQTVDHFG--KLDILVNNAAEQHPQDSILNISTEQLEKTFRTNIFSMFHMTKKALPHLQEGCA---IINTTSITAYEGDTALIDYSSTKGAIVSFTRSMAKSLADKGIRVNAVAPGPIWTP--LIPATFPEEK---------VKQHGLDTPMGRPGQPVEHAGAYVLLASDESSYMTGQTIHVNGGRFIST----------------
+>Q5KTS5.1
+MASGGQFP----PQKQESQPGKEHLMDPSPQHASPHYKPANKLQGKVALVTGGDSGIGRSVCYHFALEGATVAFTFVKGHEDKDANETLELLRKAKSSDAKDPIAIAADLGFDDNCKKVVDQVVNAFG--SIDVLVNNAAEQYKASTVEDIDEERLERVFRTNIFAYFFMARHALKHMREGST---IINTTSINAYKGNAKLLDYTATKGAIVAFTRGLSLQLISKGIRVNGVAPGPVWTP--LIPSSFDEEE---------VKQFGSEVPMKRAGQPYEIATAYVFLASCDSSYYSGQVLHPNGGAIVNG----------------
+>Q49117.2
+---------------------------------------MSKLEGKVAVVTGASKGIGAAIAKALAKDGAAVVVNYAS--SKAGADAVVEAITAA----GGKAIAVQADVSQAVQARGLVEAAVQQFG--RLDVLVN-NSGVYEFAAIEEVTEEHYRRIFDVNVLGVLLATQAASKHLGEGGS---IINISSVVTDVLMPTSAVYSGTKGALNAISGVLANELAPRKIRVNVVSPGYVVTEGTHTAGIAGSEM---------EAGLVAQTPLGRSGQPDDIAGVVAFLASDDARWVTGEVINASGGVR-------------------
+>target
+----------------------------------------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEI---GP-------AACAIALDVTDQASIDRCVAELLDRWG--SIDILVNNAALFDLAP-IVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFAD-YENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-----------------
+>Q59787.1
+----------------------------------------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEI---GP-------AACAIALDVTDQASIDRCVAELLDRWG--SIDILVNNAALFDLAP-IVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFAD-YENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-----------------
+>Q48436.2
+-------------------------------------------MKKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATAKAVASEINQAGG-------RAMAVKVDVSDRDQVFAAVEQARKTLG--GFDVIVNNAGVAPSTP-IESITPEIVDKVYNINVKGVIWGIQAAVEAFKKEGHGGKIINACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGYCPGIVKTPMWAEIDRQVSE-AAGKPLGYGTAEFAKRITLGRLSEPEDVAACVSYLASPDSDYMTGQSLLIDGGMVFN-----------------
+>Q04520.1
+-------------------------------------------MQKVALVTGAGQGIGKAIALRLVKDGFAVAIADYNDATATAVAAEINQAGG-------RAVAIKVDVSRRDQVFAAVEQARKALG--GFNVIVNNAGIAPSTP-IESITEEIVDRVYNINVKGVIWGMQAAVEAFKKEGHGGKIVNACSQAGHVGNPELAVYSSSKFAVRGLTQTAARDLAPLGITVNGFCPGIVKTPMWAEIDRQCRK-RRAN--RWATARLN-------LPNASPLAACRSLKTSPPACRSSPARIPTI-----------------------
+>P66776.1
+-----------------------------------------MTNNKVALVTGGAQGIGFKIAERLVEDGFKVAVVDFNEEGAKAAALKLSSDGT-------KAIAIKADVSNRDDVFNAVRQTAAQFG--DFHVMVNNAGLGPTTP-IDTITEEQFKTVYGVNVAGVLWGIQAAHEQFKKFNHGGKIINATSQAGVEGNPGLSLYCSTKFAVRGLTQVAAQDLASEGITVNAFAPGIVQTPMMESIAVATAE-EAGKPEAWGWEQFTSQIALGRVSQPEDVSNVVSFLAGKDSDYITGQTIIVDGGMRFR-----------------
+>Q5HKG6.1
+-------------------------------------------MSKTAIITGSAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGY-------QAVAFKSDVSKKKEQEELVQFAVTEFG--QLDVMVNNAGVDAVTP-ILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR-----------------
+>Q8CQD2.1
+-------------------------------------------MSKTAIITGAAGGLGKGIAERLANDGFNIVLQDINEALLLETEKEFKEKGY-------QAVAYKSDVSKKKEQEELVQFAVTEFG--QLDVMVNNAGVDAVTP-ILEIGEEELSKLFNINVFGTLFGIQAAANQFIKQKSKGKIINACSIAGHESYEVLGTYSATKHSVRSFTQTAAKELADKGITVNAYCPGVAKTEMWDRIDEEMVKLDDSLEIGDAFEAFSSEIKLGRYQEPSDVANLVSFLASNDSDYITGQSILTDGGLVYR-----------------
+>Q1JP75.1
+--------------------------------------MDLRLAGRRALVTGAGKGIGRSIVKALHAAGARVVAVSRTQADLDSLVRECP-----------GVETVCVDLAD----WEATEQALGGVG--PVDLLVNNAAVAFLQP-FLEVTKEAYDMSFSVNLRAVIQVSQIVARGLIARGAPGVIVNVSSQASQRGLTNHSVYCSTKGALDTLTKVMAVELGPHKIRVNAVNPTVVMTPMGQAAWSDPQK----------AKAMLDRIPLGRFAEVENVVDTILFLLSDRSSMTTGSTVPVDGGFLAT-----------------
+>Q91XV4.1
+--------------------------------------MDLGLAGRRALVTGAGKGIGRSTVLALQAAGAHVVAVSRTQADLDSLVSECP-----------GVETVCVDLAD----WEATEQALSSVG--PVDLLVNNAAVALLQP-FLEVTKEAFDMSFNVNLRAVIQVSQIVARGMIARGAPGAIVNVSSQASQRALANHSVYCSTKGALDMLTKMMALELGPHKIRVNAVNPTVVMTSMGRTNWSDPHK----------AKVMLDRIPLGKFAEVENVVDAILFLLSHRSNMTTGSTLPVDGGFLVT-----------------
+>Q7Z4W1.2
+--------------------------------------MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECP-----------GIEPVCVDLGD----WEATERALGSVG--PVDLLVNNAAVALLQP-FLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHK----------AKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC-----------------

modules/bindings/tests/testfiles/pairwise_aln.fasta

+>testseq
+------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADIN---LEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTE----RLVADEEFTDWLCKR-----TPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL

modules/bindings/tests/testfiles/similar.fasta

+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRGKIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATEMTERLVADEEFTDWLCKRTPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL

modules/bindings/tests/testfiles/test.fasta

+>testseq
+MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADINLEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS