from __future__ import absolute_import, division, print_function from iotbx import bioinformatics import unittest import sys from six.moves import zip residue_basket="ACCDDDEEEE" sequence1 = "VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS" sequence2 = "LVKFYGRKFVLLFMDQKTFDKYESKLETSGYEKFFIFCMASPISPA" name1 = "gi|159164330|pdb|2E6P|A" name2 = "Q8E5Q5_STRA3" description_tmplt = "Chain %s, Solution Structure Of The Ig-Like Domain" class test_sequence(unittest.TestCase): def testEquality(self): seq1 = bioinformatics.sequence( sequence = sequence1, name = name1 ) seq2 = bioinformatics.sequence( sequence = sequence1, name = name2 ) fasta1 = bioinformatics.fasta_sequence( sequence = sequence1, name = name2, description = description_tmplt % "A" ) fasta2 = bioinformatics.fasta_sequence( sequence = sequence1, name = name2, description = description_tmplt % "B" ) pir1 = bioinformatics.pir_sequence( sequence = sequence1, name = name2, type = "P1", description = description_tmplt % "C" ) self.assertEqual( seq1, seq2 ) self.assertEqual( seq1, fasta1 ) self.assertEqual( seq1, fasta2 ) self.assertEqual( seq1, pir1 ) self.assertEqual( seq2, fasta1 ) self.assertEqual( seq2, fasta2 ) self.assertEqual( seq2, pir1 ) self.assertEqual( fasta1, fasta2 ) self.assertEqual( fasta1, pir1 ) self.assertEqual( fasta2, pir1 ) def testNonEquality(self): seq1 = bioinformatics.sequence( sequence = sequence1, name = name1 ) seq2 = bioinformatics.sequence( sequence = sequence2, name = name1 ) seq3 = bioinformatics.sequence( sequence = sequence1 + "A", name = name1 ) fasta1 = bioinformatics.fasta_sequence( sequence = sequence2, name = name1, description = description_tmplt % "A" ) pir1 = bioinformatics.pir_sequence( sequence = sequence2, name = name1, type = "P1", description = description_tmplt % "A" ) self.assertTrue( seq1 != seq2 ) self.assertTrue( seq1 != seq3 ) self.assertTrue( seq1 != fasta1 ) self.assertTrue( seq1 != pir1 ) class test_fasta_sequence(unittest.TestCase): def setUp(self): self.short = bioinformatics.fasta_sequence( sequence = sequence1, name = name1, description = description_tmplt % "A" ) self.long = bioinformatics.fasta_sequence( sequence = sequence1 * 4, name = name1, description = description_tmplt % "A" ) def testFormat(self): self.assertEqual( self.short.format( 70 ), ">gi|159164330|pdb|2E6P|A Chain A, Solution Structure Of The Ig-Like Do\n" + "VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS" ) self.assertEqual( self.short.format( 20 ), ">gi|159164330|pdb|2E\n" + "VVKMDGRKHRLILPEAKVQD\n" + "SGEFECRTEGVSAFFGVTVQ\n" + "DPSGPS" ) def testStr(self): self.assertEqual( str( self.short ), ">gi|159164330|pdb|2E6P|A Chain A, Solution Structure Of The Ig-Like Do\n" + "VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS" ) self.assertEqual( str( self.long ), ">gi|159164330|pdb|2E6P|A Chain A, Solution Structure Of The Ig-Like Do\n" + "VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSGEF\n" + "ECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSVV\n" + "KMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS" ) class test_pir_sequence(unittest.TestCase): def setUp(self): self.short = bioinformatics.pir_sequence( sequence = sequence1, name = name1, type = "P1", description = description_tmplt % "A" ) self.long = bioinformatics.pir_sequence( sequence = sequence1 * 4, name = name1, type = "P1", description = description_tmplt % "A" ) def testFormat(self): self.assertEqual( self.short.format( 70 ), ">P1;gi|159164330|pdb|2E6P|A\n" + "Chain A, Solution Structure Of The Ig-Like Domain\n" + " VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS*" ) self.assertEqual( self.short.format( 20 ), ">P1;gi|159164330|pdb\n" + "Chain A, Solution St\n" + " VVKMDGRKHRLILPEAKV\n" + " QDSGEFECRTEGVSAFFG\n" + " VTVQDPSGPS*" ) def testStr(self): self.assertEqual( str( self.short ), ">P1;gi|159164330|pdb|2E6P|A\n" + "Chain A, Solution Structure Of The Ig-Like Domain\n" + " VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS*" ) self.assertEqual( str( self.long ), ">P1;gi|159164330|pdb|2E6P|A\n" + "Chain A, Solution Structure Of The Ig-Like Domain\n" + " VVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSG\n" + " EFECRTEGVSAFFGVTVQDPSGPSVVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSG\n" + " PSVVKMDGRKHRLILPEAKVQDSGEFECRTEGVSAFFGVTVQDPSGPS*" ) class test_midline(unittest.TestCase): def setUp(self): self.midline = bioinformatics.midline( identical = "#" ) def testConservationCode(self): self.assertEqual( self.midline.conservation_code( [ "A", "A", "A", "A" ] ), self.midline.identical ) self.assertEqual( self.midline.conservation_code( [ "A", "A", "A", "B" ] ), self.midline.differ ) def testMidline(self): self.assertEqual( self.midline.compare( [ "ABCD-EFGH", "ABD--EKGH" ] ), "## # ##" ) self.assertEqual( self.midline.compare( [] ), "" ) ali_1hml = "-KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR" ali_1hfy = "-EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR" ali_1ghl = "GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK" ali_1lz3 = "-KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK" ali_empt = "---------------------------------------------------------------------------" class test_alignment(unittest.TestCase): def setUp(self): self.alignment1 = bioinformatics.alignment( alignments = [ ali_1hml, ali_1hfy ], names = [ "1hml", "1hfy" ] ) self.alignment2 = bioinformatics.alignment( alignments = [ ali_1hml, ali_1hfy, ali_1ghl, ali_1lz3 ], names = [ "1hml", "1hfya", "1ghla", "1lz3" ] ) self.alignment3 = bioinformatics.alignment( alignments = [], names = [] ) self.alignment4 = bioinformatics.alignment( alignments = [ ali_1hfy, ali_1ghl, ali_empt ], names = [ "1hfya", "1ghla", "empty" ] ) def test_error(self): self.assertRaises( ValueError, bioinformatics.alignment, [ ali_1hml, ali_1hml + "A" ], [ "1hml", "1hfy" ] ) self.assertRaises( ValueError, bioinformatics.alignment, [ ali_1hml, ali_1hml ], [ "1hml", "1hfy", "1ghla" ] ) def test_identity_count(self): self.assertEqual( self.alignment1.identity_count(), 49 ) self.assertEqual( self.alignment2.identity_count(), 21 ) self.assertEqual( self.alignment3.identity_count(), 0 ) self.assertEqual( self.alignment4.identity_count(), 0 ) def test_identity_fraction(self): self.assertAlmostEqual( self.alignment1.identity_fraction(), 0.700, 3 ) self.assertAlmostEqual( self.alignment2.identity_fraction(), 0.300, 3 ) self.assertAlmostEqual( self.alignment3.identity_fraction(), 1.000, 3 ) self.assertAlmostEqual( self.alignment4.identity_fraction(), 1.000, 3 ) def test_multiplicity(self): self.assertEqual( self.alignment1.multiplicity(), 2 ) self.assertEqual( self.alignment2.multiplicity(), 4 ) self.assertEqual( self.alignment3.multiplicity(), 0 ) self.assertEqual( self.alignment4.multiplicity(), 3 ) def test_length(self): self.assertEqual( self.alignment1.length(), 75 ) self.assertEqual( self.alignment2.length(), 75 ) self.assertEqual( self.alignment3.length(), 0 ) self.assertEqual( self.alignment4.length(), 75 ) def test_copy(self): c = self.alignment1.copy( alignments = [ "AB", "BA" ], names = [ "XY", "YX" ], gap = "#" ) self.assertTrue( c is not self.alignment1 ) self.assertEqual( c.alignments, [ "AB", "BA" ] ) self.assertEqual( c.names, [ "XY", "YX" ] ) self.assertEqual( c.gap, "#" ) def test__str__(self): self.assertEqual( str( self.alignment1 ), ">1hml\n" + "-KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKSSQ\n" + "VPQSR\n\n" + ">1hfy\n" + "-EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKDDQ\n" + "NPHSR" ) def test_extend(self): sequences = [ "ABKQFTKCELSQLLKDIDGYGGIALPELICTMFHTSGYDTQAIVENNESTEYGLFQISNKLWCKSSQVPQSRNOPQR", "CDEEQLTKCEVFQKLKDLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNNDSTEYGLFQINNKIWCKDDQNPHSRSTUV", "FGHIGKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNTDGSTDYGILQINSRWWCNDGRTPGSKXYZ", "JKILMKVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNTDGSTDYGILQINSRWWCNDGRTPGSKAB", ] ali = self.alignment2.copy() ali.extend( sequences = sequences ) self.assertEqual( ali.names, self.alignment2.names ) self.assertEqual( ali.gap, self.alignment2.gap ) self.assertEqual( ali.alignments, [ "AB------------" + self.alignment2.alignments[0] + "NOPQR---------", "--CDE---------" + self.alignment2.alignments[1] + "-----STUV-----", "-----FGHI-----" + self.alignment2.alignments[2] + "---------XYZ--", "---------JKILM" + self.alignment2.alignments[3] + "------------AB", ] ) class test_fasta_alignment(unittest.TestCase): def setUp(self): self.alignment = bioinformatics.fasta_alignment( alignments = [ ali_1hml, ali_1hfy, ali_1ghl, ali_1lz3 ], names = [ "1hml", "1hfya", "1ghla", "1lz3" ], descriptions = [ "alpha lactalbumin:Homo sapiens", "alpha-lactalbumin:Capra hircus", "lysozyme:Phasianus colchicus", "lysozyme:Meleagris gallopavo", ] ) def test_error(self): self.assertRaises( ValueError, bioinformatics.fasta_alignment, [ ali_1hml, ali_1hml ], [ "1hml", "1hfy" ], [ "alpha lactalbumin:Homo sapiens", "alpha-lactalbumin:Capra hircus", "lysozyme:Phasianus colchicus", ] ) def test_format(self): self.assertEqual( self.alignment.format( 40 ), ">1hml alpha lactalbumin:Homo sapiens\n" + "-KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYD\n" + "TQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR\n\n" + ">1hfya alpha-lactalbumin:Capra hircus\n" + "-EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYD\n" + "TQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR\n\n" + ">1ghla lysozyme:Phasianus colchicus\n" + "GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFN\n" + "TGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK\n\n" + ">1lz3 lysozyme:Meleagris gallopavo\n" + "-KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFD\n" + "THATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK" ) def test__str__(self): self.assertEqual( str( self.alignment ), ">1hml alpha lactalbumin:Homo sapiens\n" + "-KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKSSQ\n" + "VPQSR\n\n" + ">1hfya alpha-lactalbumin:Capra hircus\n" + "-EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKDDQ\n" + "NPHSR\n\n" + ">1ghla lysozyme:Phasianus colchicus\n" + "GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQINSRWWCNDGR\n" + "TPGSK\n\n" + ">1lz3 lysozyme:Meleagris gallopavo\n" + "-KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQINSRWWCNDGR\n" + "TPGSK" ) def test_copy(self): c = self.alignment.copy( descriptions = [ "A", "B", "C", "D" ] ) self.assertEqual( c.descriptions, [ "A", "B", "C", "D" ] ) self.assertEqual( c.alignments, self.alignment.alignments ) self.assertEqual( c.names, self.alignment.names ) self.assertEqual( c.gap, self.alignment.gap ) class test_pir_alignment(unittest.TestCase): def setUp(self): self.alignment = bioinformatics.pir_alignment( alignments = [ ali_1hml, ali_1hfy, ali_1ghl, ali_1lz3 ], names = [ "1hml", "1hfya", "1ghla", "1lz3" ], types = [ "P1" ] * 4, descriptions = [ "alpha lactalbumin:Homo sapiens", "alpha-lactalbumin:Capra hircus", "lysozyme:Phasianus colchicus", "lysozyme:Meleagris gallopavo", ] ) def test_error(self): self.assertRaises( ValueError, bioinformatics.pir_alignment, [ ali_1hml, ali_1hml ], [ "1hml", "1hfy" ], [ "P1", "P1", "P1" ], [ "alpha lactalbumin:Homo sapiens", "alpha-lactalbumin:Capra hircus", ] ) self.assertRaises( ValueError, bioinformatics.pir_alignment, [ ali_1hml, ali_1hml ], [ "1hml", "1hfy" ], [ "P1", "P1" ], [ "alpha lactalbumin:Homo sapiens", "alpha-lactalbumin:Capra hircus", "lysozyme:Phasianus colchicus", ] ) def test_format(self): self.assertEqual( self.alignment.format( 40 ), ">P1;1hml\nalpha lactalbumin:Homo sapiens\n" + " -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSG\n" + " YDTQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR*\n\n" + ">P1;1hfya\nalpha-lactalbumin:Capra hircus\n" + " -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSG\n" + " YDTQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR*\n\n" + ">P1;1ghla\nlysozyme:Phasianus colchicus\n" + " GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESN\n" + " FNTGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK*\n\n" + ">P1;1lz3\nlysozyme:Meleagris gallopavo\n" + " -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESN\n" + " FDTHATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK*" ) def test__str__(self): self.assertEqual( str( self.alignment ), ">P1;1hml\nalpha lactalbumin:Homo sapiens\n" + " -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQISNKLWCKS\n" + " SQVPQSR*\n\n" + ">P1;1hfya\nalpha-lactalbumin:Capra hircus\n" + " -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQINNKIWCKD\n" + " DQNPHSR*\n\n" + ">P1;1ghla\nlysozyme:Phasianus colchicus\n" + " GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQINSRWWCND\n" + " GRTPGSK*\n\n" + ">P1;1lz3\nlysozyme:Meleagris gallopavo\n" + " -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQINSRWWCND\n" + " GRTPGSK*" ) def test_copy(self): c = self.alignment.copy( descriptions = [ "A", "B", "C", "D" ], types = [ "P1", "P2", "P3", "P4" ] ) self.assertEqual( c.descriptions, [ "A", "B", "C", "D" ] ) self.assertEqual( c.types, [ "P1", "P2", "P3", "P4" ] ) self.assertEqual( c.alignments, self.alignment.alignments ) self.assertEqual( c.names, self.alignment.names ) self.assertEqual( c.gap, self.alignment.gap ) class test_clustal_alignment(unittest.TestCase): def setUp(self): self.alignment = bioinformatics.clustal_alignment( alignments = [ ali_1hml, ali_1hfy, ali_1ghl, ali_1lz3 ], names = [ "1hml", "1hfya", "1ghla", "1lz3" ], program = "CLUSTAL X 1.35" ) def test_format(self): self.assertEqual( self.alignment.format( 40, 10 ), "CLUSTAL X 1.35 multiple sequence alignment\n\n" + "1hml -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYD 37\n" + "1hfya -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYD 37\n" + "1ghla GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFN 40\n" + "1lz3 -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFD 39\n" + " ** * * * * * * \n\n" + "1hml TQAIVENN--ESTEYGLFQISNKLWCKSSQVPQSR 70\n" + "1hfya TQAIVQNN--DSTEYGLFQINNKIWCKDDQNPHSR 70\n" + "1ghla TGATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK 74\n" + "1lz3 THATNRNT-DGSTDYGILQINSRWWCNDGRTPGSK 73\n" + " * * * ** ** ** ** * * " ) def test__str__(self): self.assertEqual( str( self.alignment ), "CLUSTAL X 1.35 multiple sequence alignment\n\n" + "1hml -KQFTKCELSQLLK--DIDGYGGIALPELICTMFHTSGYDTQAIVENN--ESTEYGLFQI 55\n" + "1hfya -EQLTKCEVFQKLK--DLKDYGGVSLPEWVCTAFHTSGYDTQAIVQNN--DSTEYGLFQI 55\n" + "1ghla GKVYGRCELAAAMKRMGLDNYRGYSLGNWVCAAKFESNFNTGATNRNT-DGSTDYGILQI 59\n" + "1lz3 -KVYGRCELAAAMKRLGLDNYRGYSLGNWVCAAKFESNFDTHATNRNT-DGSTDYGILQI 58\n" + " ** * * * * * * * * * ** ** **\n\n" + "1hml SNKLWCKSSQVPQSR 70\n" + "1hfya NNKIWCKDDQNPHSR 70\n" + "1ghla NSRWWCNDGRTPGSK 74\n" + "1lz3 NSRWWCNDGRTPGSK 73\n" + " ** * * " ) def test_copy(self): c = self.alignment.copy( program = "Foo" ) self.assertEqual( c.program, "Foo" ) self.assertEqual( c.alignments, self.alignment.alignments ) self.assertEqual( c.names, self.alignment.names ) self.assertEqual( c.gap, self.alignment.gap ) seq = """ Error >chain_A TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG GGFSEVIFR > chain A TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG GGFSEVIFR > chain_A TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG GGFSEVIFR* > TPDCVTGKVE YTKYNDDDTF TVKVGDKELF TNRWNLQSLL LSAQITGMTV TIKTNACHNG GGFSEVIFR >chain_A""" seq_sequence = "TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR" fasta = """ Error >FOSB_MOUSE Protein fosB. 338 bp MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL > FOSB_MOUSE Protein fosB. 338 bp MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL > 1YJP:A|PDBID|CHAIN|SEQUENCE MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL """ fasta_sequence = ( "MFQAFPGDYDSGSRCSSSPSAESQYLSSVDSFGSPPTAAASQECAGLGEMPGSFVPTVTA" + "ITTSQDLQWLVQPTLISSMAQSQGQPLASQPPAVDPYDMPGTSYSTPGLSAYSTGGASGS" + "GGPSTSTTTSGPVSARPARARPRRPREETLTPEEEEKRRVRRERNKLAAAKCRNRRRELT" + "DRLQAETDQLEEEKAELESEIAELQKEKERLEFVLVAHKPGCKIPYEEGPGPGPLAEVRD" + "LPGSTSAKEDGFGWLLPPPPPPPLPFQSSRDAPPNLTASLFTHSEVQVLGDPFPVVSPSY" + "TSSFVLTCPEVSAFAGAQRTSGSEQPSDPLNSPSLLAL" ) pir = """ Error >P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P1;CRAB_ANAPL MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK > P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P11;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P1;CRAB_ ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* """ tolerant_pir = """ Error >P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* Error2 >CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >CRAB_ANAPL MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK """ tf = """ > anb.pdb AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTT TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKV GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLL IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINK DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAA VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEY GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASK ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVG KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLE AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVA QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKL ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQ YAASVAGLMITTECMVTDLP AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVAST ATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVG KEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLI IAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKD TTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAV EEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGKGGDGNYGYNAATEEYGNMIDMGILDP TKVTRSALQYAASVAGLMITTECMVTDLP """ lineseparated = """ AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTT TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKV GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLL IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINK DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAA VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEY GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASK ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVG KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLE AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVA QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKL ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQ YAASVAGLMITTECMVTDLP """ dbfetch = """ >PDB:1GAG_A VFPSSVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESAS LRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAEN NPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDI XETDXXRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQ VLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFF HSEENK >PDB:1GAG_B PATGDFMNMSPVG """ pir_sequence = ( "MDITIHNPLIRRPLFSWLAPSRIFDQIFGEHLQESELLPASPSLSPFLMR" + "SPIFRMPSWLETGLSEMRLEKDKFSVNLDVKHFSPEELKVKVLGDMVEIH" + "GKHEERQDEHGFIAREFNRKYRIPADVDPLTITSSLSLDGVLTVSAPRKQ" + "SDVPERSIPITREEKPAIAGAQRK" ) # Break string to preserve syntactic whitespace clustal1 = ( """CLUSTAL 2.0.10 multiple sequence alignment Horse VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA--- 57 chain_A VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED 60 *** .: * .*:** .... :* : * *:* ..* * * :*. : .*::** \n""" + """ Horse ---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLP 114 chain_A LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP 120 ** .* ** : : .. . *. *:: ** * :: ::::*..:: .* : * Horse NDFTPAVHASLDKFLSSVSTVLTSKYR------ 141 chain_A GDFGADAQGAMNKALELFRKDIAAKYKELGYQG 153 .** . .:.:::* *. . . :::**: """ ) clustal2 = """CLUSTAL X (1.81) multiple sequence alignment 1vkk VVCEVDPELKETLRKFRFR---KETNNAAIIMKVD--KDRQMVVLEDELQ-NISPEELKL 1ahq -GIAVSDDCVQKFNELKLGHQH-----RYVTFKMNASN--TEVVVEHVGGPNATYEDFKS 1vkk ELPERQPRFVVYSYKYVH--DDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAE- 1ahq QLPERDCRYAIFDYEFQVDG---GQRNKITFILWAPDSAPIKSKMMYTSTKDSIKKKLVG 1vkk L-TKVFEIRTTDD-LTETWLKEKLAFFR 1ahq IQ-VEVQATD-AAEISEDAVSERAKK-- """ clustal3 = """MUSCLE (3.8) multiple sequence alignment 1mru_A -----------------GSHMTTPSHLSD-----RYELGEILGFGGMSEVHLARDLRLHR 2h34_A MGSSHHHHHHSSGLVPRGSHMDGTAESREGTQFGPYRLRRLVGRGGMGDVYEAEDTVRER **** .: : * * ::* ***.:*: * * * 1mru_A DVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYV 2h34_A IVALKLMSETLSSDPVFRTRMQREARTAGRLQEPHVVPIHDFGEID---GQL-YVDMRLI **:*:: *: ** * *:.***..*. *: * :*.::* ** : * * *: * : """ bad_clustal1 = """MUSCLE (3.8) multiple sequence alignment Blah 1mru_A -----------------GSHMTTPSHLSD-----RYELGEILGFGGMSEVHLARDLRLHR 2h34_A MGSSHHHHHHSSGLVPRGSHMDGTAESREGTQFGPYRLRRLVGRGGMGDVYEAEDTVRER **** .: : * * ::* ***.:*: * * * 1mru_A DVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYV 2h34_A IVALKLMSETLSSDPVFRTRMQREARTAGRLQEPHVVPIHDFGEID---GQL-YVDMRLI **:*:: *: ** * *:.***..*. *: * :*.::* ** : * * *: * : """ bad_clustal2 = """MUSCLE (3.8) multiple sequence alignment 1mru_A -----------------GSHMTTPSHLSD-----RYELGEILGFGGMSEVHLARDLRLHR 2h34_A MGSSHHHHHHSSGLVPRGSHMDGTAESREGTQFGPYRLRRLVGRGGMGDVYEAEDTVRER **** .: : * * ::* ***.:*: * * * 1mru_A DVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYV 2h34_A IVALKLMSETLSSDPVFRTRMQREARTAGRLQEPHVVPIHDFGEID---GQL-YVDMRLI 2ghj_A IVALKLMSETLSSDPVFRTRMQREARTAGRLQEPHVVPIHDFGEID---GQL-YVDMRLI **:*:: *: ** * *:.***..*. *: * :*.::* ** : * * *: * : """ pir_ali1 = """ >P1;Horse VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA--- ---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLP NDFTPAVHASLDKFLSSVSTVLTSKYR------* >P3;chain_A VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP GDFGADAQGAMNKALELFRKDIAAKYKELGYQG* """ fasta_ali1 = """ >2QZU:A Putative sulfatase from B. fragilis QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYP VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQ GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWI AYGTYDY-----------------------------H-LKPXYWNTTAPR DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXN PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP--- -------------------AKG----------------------TEXGDY FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG-- ---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDP --LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQ PYYFVKF--------DNHA------------------TGYRGLRTDRYTY AVHAT-DGK------------------------IDNVILFDRTNDPHEXN NIASQ--QLKLTHTFNRQLKTWLEKTNDPF >3B5Q:B Putative sulfatase from B. thetaiotaomicron -EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCP LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSES GYEAVHFGKTHDX---------------------------GSLRGFKHKE P------------------------------------------------- ---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQ NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVED WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEEN YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA-- ---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPV DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYV VSEWHSEYEYVT-------------------------TPGRXVRGPRYKY THYLE----------------------------GNGEELYDXKKDPGERK NLAKDPKYSKILAEHRALLDDYITRSKDDY """ ali_ali1 = """ >2QZU:A QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYP VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQ GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWI AYGTYDY-----------------------------H-LKPXYWNTTAPR DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXN PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP--- -------------------AKG----------------------TEXGDY FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG-- ---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDP --LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQ PYYFVKF--------DNHA------------------TGYRGLRTDRYTY AVHAT-DGK------------------------IDNVILFDRTNDPHEXN NIASQ--QLKLTHTFNRQLKTWLEKTNDPF >3B5Q:B -EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCP LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSES GYEAVHFGKTHDX---------------------------GSLRGFKHKE P------------------------------------------------- ---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQ NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVED WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEEN YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA-- ---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPV DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYV VSEWHSEYEYVT-------------------------TPGRXVRGPRYKY THYLE----------------------------GNGEELYDXKKDPGERK NLAKDPKYSKILAEHRALLDDYITRSKDDY """ class test_sequence_parse(unittest.TestCase): def testSequence(self): ( sequences, unknowns ) = bioinformatics.seq_sequence_parse( seq ) self.assertEqual( len( sequences ), 4 ) self.assertEqual( unknowns, [ "\nError\n", ">chain_A" ] ) self.assertEqual( sequences[0].name, "chain_A" ) self.assertEqual( sequences[0].sequence, seq_sequence ) self.assertEqual( sequences[1].name, "chain A" ) self.assertEqual( sequences[1].sequence, seq_sequence ) self.assertEqual( sequences[2].name, "chain_A" ) self.assertEqual( sequences[2].sequence, seq_sequence ) self.assertEqual( sequences[3].name, '' ) self.assertEqual( sequences[3].sequence, seq_sequence ) ( fastas, unknowns ) = bioinformatics.seq_sequence_parse( fasta ) self.assertEqual( len( fastas ), 3 ) self.assertEqual( unknowns, [ "\nError\n" ] ) self.assertEqual( fastas[0].name, "FOSB_MOUSE Protein fosB. 338 bp" ) self.assertEqual( fastas[0].sequence, fasta_sequence ) self.assertEqual( fastas[1].name, "FOSB_MOUSE Protein fosB. 338 bp" ) self.assertEqual( fastas[1].sequence, fasta_sequence ) self.assertEqual( fastas[2].name, "1YJP:A|PDBID|CHAIN|SEQUENCE" ) self.assertEqual( fastas[2].sequence, fasta_sequence ) def testFasta(self): ( fastas, unknowns ) = bioinformatics.fasta_sequence_parse( fasta ) self.assertEqual( len( fastas ), 3 ) self.assertEqual( unknowns, [ "\nError\n", ] ) self.assertEqual( fastas[0].name, "FOSB_MOUSE" ) self.assertEqual( fastas[0].sequence, fasta_sequence ) self.assertEqual( fastas[0].description, "Protein fosB. 338 bp" ) self.assertEqual( fastas[1].name, "FOSB_MOUSE" ) self.assertEqual( fastas[1].sequence, fasta_sequence ) self.assertEqual( fastas[1].description, "Protein fosB. 338 bp" ) self.assertEqual( fastas[2].name, "1YJP" ) self.assertEqual( fastas[2].description, "A|PDBID|CHAIN|SEQUENCE" ) self.assertEqual( fastas[2].sequence, fasta_sequence ) def testPir(self): ( pirs, unknowns ) = bioinformatics.pir_sequence_parse( pir ) self.assertEqual( len( pirs ), 2 ) self.assertEqual( unknowns, [ "\nError\n", pir[490:] ] ) self.assertEqual( pirs[0].name, "CRAB_ANAPL" ) self.assertEqual( pirs[0].type, "P1" ) self.assertEqual( pirs[0].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN)." ) self.assertEqual( pirs[0].sequence, pir_sequence ) self.assertEqual( pirs[1].name, "CRAB_ANAPL" ) self.assertEqual( pirs[1].type, "P1" ) self.assertEqual( pirs[1].description, "" ) self.assertEqual( pirs[1].sequence, pir_sequence ) def testTolerantPir(self): ( pirs, unknowns ) = bioinformatics.tolerant_pir_sequence_parse( tolerant_pir ) self.assertEqual( len( pirs ), 3 ) self.assertEqual( unknowns, [ "\nError\n", "Error2\n\n" ] ) self.assertEqual( pirs[0].name, "P1;CRAB_ANAPL" ) self.assertEqual( pirs[0].type, "P1" ) self.assertEqual( pirs[0].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN)." ) self.assertEqual( pirs[0].sequence, pir_sequence ) self.assertEqual( pirs[1].name, "CRAB_ANAPL" ) self.assertEqual( pirs[1].type, "P1" ) self.assertEqual( pirs[1].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN)." ) self.assertEqual( pirs[1].sequence, pir_sequence ) self.assertEqual( pirs[2].name, "CRAB_ANAPL" ) self.assertEqual( pirs[2].type, "P1" ) self.assertEqual( pirs[2].description, "" ) self.assertEqual( pirs[2].sequence, pir_sequence ) def test_tf_parse(self): ( seqs, unknowns ) = bioinformatics.tf_sequence_parse( text = tf ) self.assertEqual( unknowns, [] ) self.assertEqual( len( seqs ), 3 ) self.assertEqual( seqs[0].name, "anb.pdb" ) self.assertEqual( seqs[0].sequence, "AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTT" + "TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKV" + "GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLL" + "IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINK" + "DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAA" + "VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEY" + "GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP" ) self.assertEqual( seqs[1].name, "anb.pdb" ) self.assertEqual( seqs[1].sequence, "AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASK" + "ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVG" + "KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLE" + "AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVA" + "QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKL" + "ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQ" + "YAASVAGLMITTECMVTDLP" ) self.assertEqual( seqs[2].name, "anb.pdb" ) self.assertEqual( seqs[2].sequence, "AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVAST" + "ATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVG" + "KEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLI" + "IAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKD" + "TTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAV" + "EEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGKGGDGNYGYNAATEEYGNMIDMGILDP" + "TKVTRSALQYAASVAGLMITTECMVTDLP" ) def test_ls_parse(self): ( seqs, unknowns ) = bioinformatics.lineseparated_sequence_parse.parse( text = lineseparated, name = "foo" ) self.assertEqual( unknowns, [] ) self.assertEqual( len( seqs ), 2 ) self.assertEqual( seqs[0].name, "foo" ) self.assertEqual( seqs[0].sequence, "AAKDVKFGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTT" + "TATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKV" + "GKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLL" + "IIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINK" + "DTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAA" + "VEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEY" + "GNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLP" ) self.assertEqual( seqs[1].name, "foo" ) self.assertEqual( seqs[1].sequence, "AAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASK" + "ANDAAGDGTTTATVLAQAIITEGLKAVAAGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVG" + "KLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLE" + "AVAKAGKPLLIIAEDVEGEALQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVA" + "QIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKL" + "ADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQ" + "YAASVAGLMITTECMVTDLP" ) def test_dbfetch_parse(self): ( seqs, unknowns ) = bioinformatics.dbfetch_sequence_parse( text = dbfetch ) self.assertEqual( unknowns, [] ) self.assertEqual( len( seqs ), 2 ) self.assertEqual( seqs[0].name, "1GAG" ) self.assertEqual( seqs[0].chain, "A" ) self.assertEqual( seqs[0].sequence, "VFPSSVFVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESAS" + "LRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAEN" + "NPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDI" + "XETDXXRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQ" + "VLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPKMRPTFLEIVNLLKDDLHPSFPEVSFF" + "HSEENK" ) self.assertEqual( seqs[1].name, "1GAG" ) self.assertEqual( seqs[1].chain, "B" ) self.assertEqual( seqs[1].sequence, "PATGDFMNMSPVG" ) def test_filename_selection(self): self.assertEqual( bioinformatics.sequence_parser_for( "dummy.pir" ), bioinformatics.pir_sequence_parse ) self.assertEqual( bioinformatics.sequence_parser_for( "seq" ), None ) def test_known_formats(self): self.assertEqual( sorted( bioinformatics.known_sequence_formats() ), ['.dat', '.fa', '.faa', '.fasta', '.pir', '.seq'] ) class test_alignment_parse(unittest.TestCase): def testClustal(self): ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( clustal1 ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.program, "CLUSTAL 2.0.10" ) self.assertEqual( ali.names, [ "Horse", "chain_A" ] ) self.assertEqual( ali.alignments, [ "VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA---" + "---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLP" + "NDFTPAVHASLDKFLSSVSTVLTSKYR------", "VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED" + "LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP" + "GDFGADAQGAMNKALELFRKDIAAKYKELGYQG" ] ) ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( clustal2 ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.program, "CLUSTAL X (1.81)" ) self.assertEqual( ali.names, [ "1vkk", "1ahq" ] ) self.assertEqual( ali.alignments, [ "VVCEVDPELKETLRKFRFR---KETNNAAIIMKVD--KDRQMVVLEDELQ-NISPEELKL" + "ELPERQPRFVVYSYKYVH--DDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNRLVQTAE-" + "L-TKVFEIRTTDD-LTETWLKEKLAFFR", "-GIAVSDDCVQKFNELKLGHQH-----RYVTFKMNASN--TEVVVEHVGGPNATYEDFKS" + "QLPERDCRYAIFDYEFQVDG---GQRNKITFILWAPDSAPIKSKMMYTSTKDSIKKKLVG" + "IQ-VEVQATD-AAEISEDAVSERAKK--" ] ) ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( clustal3 ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.program, "MUSCLE (3.8)" ) self.assertEqual( ali.names, [ "1mru_A", "2h34_A" ] ) self.assertEqual( ali.alignments, [ "-----------------GSHMTTPSHLSD-----RYELGEILGFGGMSEVHLARDLRLHR" + "DVAVKVLRADLARDPSFYLRFRREAQNAAALNHPAIVAVYDTGEAETPAGPLPYIVMEYV", "MGSSHHHHHHSSGLVPRGSHMDGTAESREGTQFGPYRLRRLVGRGGMGDVYEAEDTVRER" + "IVALKLMSETLSSDPVFRTRMQREARTAGRLQEPHVVPIHDFGEID---GQL-YVDMRLI", ] ) # Bad format badaln = "Blah\nBlah\n" + clustal2 ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( badaln ) self.assertEqual( unknowns, badaln ) self.assertEqual( ali, None ) ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( bad_clustal1 ) self.assertEqual( unknowns, bad_clustal1 ) self.assertEqual( ali, None ) ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( bad_clustal2 ) self.assertEqual( unknowns, bad_clustal2 ) self.assertEqual( ali, None ) # Empty alignment ( ali, unknowns ) = bioinformatics.clustal_alignment_parse( "CLUSTAL 2.0.10 multiple sequence alignment\n\n" ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.program, "CLUSTAL 2.0.10" ) self.assertEqual( ali.names, [] ) self.assertEqual( ali.alignments, [] ) def testPir(self): ( ali, unknowns ) = bioinformatics.pir_alignment_parse( pir_ali1 ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.names, [ "Horse", "chain_A" ] ) self.assertEqual( ali.types, [ "P1", "P3" ] ) self.assertEqual( ali.descriptions, [ "", "" ] ) self.assertEqual( ali.alignments, [ "VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKA---" + "---HGKKVGDALTLAVGHLDDLPGALSDLSNLHAHKLRVDPVNFKLLSHCLLSTLAVHLP" + "NDFTPAVHASLDKFLSSVSTVLTSKYR------", "VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED" + "LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP" + "GDFGADAQGAMNKALELFRKDIAAKYKELGYQG" ] ) # Bad format ( ali, unknowns ) = bioinformatics.pir_alignment_parse( "\n" + clustal2 ) self.assertEqual( unknowns, "\n" + clustal2 ) self.assertEqual( ali, None ) # Empty alignment ( ali, unknowns ) = bioinformatics.pir_alignment_parse( "" ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.names, [] ) self.assertEqual( ali.types, [] ) self.assertEqual( ali.descriptions, [] ) self.assertEqual( ali.alignments, [] ) def testFasta(self): ( ali, unknowns ) = bioinformatics.fasta_alignment_parse( fasta_ali1 ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.names, [ "2QZU:A", "3B5Q:B" ] ) self.assertEqual( ali.descriptions, [ "Putative sulfatase from B. fragilis", "Putative sulfatase from B. thetaiotaomicron", ] ) self.assertEqual( ali.alignments, [ "QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYP" + "VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQ" + "GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWI" + "AYGTYDY-----------------------------H-LKPXYWNTTAPR" + "DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXN" + "PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP---" + "-------------------AKG----------------------TEXGDY" + "FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG--" + "---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDP" + "--LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQ" + "PYYFVKF--------DNHA------------------TGYRGLRTDRYTY" + "AVHAT-DGK------------------------IDNVILFDRTNDPHEXN" + "NIASQ--QLKLTHTFNRQLKTWLEKTNDPF", "-EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCP" + "LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSES" + "GYEAVHFGKTHDX---------------------------GSLRGFKHKE" + "P-------------------------------------------------" + "---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQ" + "NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVED" + "WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEEN" + "YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA--" + "---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPV" + "DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYV" + "VSEWHSEYEYVT-------------------------TPGRXVRGPRYKY" + "THYLE----------------------------GNGEELYDXKKDPGERK" + "NLAKDPKYSKILAEHRALLDDYITRSKDDY", ] ) def testAli(self): ( ali, unknowns ) = bioinformatics.ali_alignment_parse( ali_ali1 ) self.assertEqual( unknowns, "" ) self.assertEqual( ali.names, [ "2QZU:A", "3B5Q:B" ] ) self.assertEqual( ali.alignments, [ "QPTPNLVFIXADQYRGDAIGCIGKEPVKTPHLDKLASEGINFTNAISSYP" + "VSSPARGXLXTGXYPIGSKVT-GNCNSETAPYGVELSQNARCWSDVLKDQ" + "GYNXGYIGKWHLDAPYKPYVDTYNNRGKVAWNEWCP---PERRHGFDHWI" + "AYGTYDY-----------------------------H-LKPXYWNTTAPR" + "DSFYYVNQ-----------WGPEYEASKAIEYINGQKDQKQPFALVVSXN" + "PPHTGYE--------------LVPDRYKEIYKDLDVEALCKGRPDIP---" + "-------------------AKG----------------------TEXGDY" + "FRNNIRNYYACITGVDENVGRIIEALKQNNLFDNTIVVFTSDHGICXG--" + "---------------AHENAGKD-IFYEESXRIPXILSWPDQIKPRKSDP" + "--LXIAFA-DLYPTLLSXXGFSKEIPETVQTFDLSNEVLTGKNKKD-LVQ" + "PYYFVKF--------DNHA------------------TGYRGLRTDRYTY" + "AVHAT-DGK------------------------IDNVILFDRTNDPHEXN" + "NIASQ--QLKLTHTFNRQLKTWLEKTNDPF", "-EKPNFLIIQCDHLTQRVVGAYGQTQGCTLPIDEVASRGVIFSNAYVGCP" + "LSQPSRAALWSGXXPHQTNVR-SNSS---EPVNTRLPENVPTLGSLFSES" + "GYEAVHFGKTHDX---------------------------GSLRGFKHKE" + "P-------------------------------------------------" + "---VAKPFTDPEFPVNNDSFLDVGTCEDAVAYLSNP--PKEPFICIADFQ" + "NPHNICGFIGENAGVHTDRPI----------SGPLPEL----PDNFDVED" + "WSNIPTPVQYICCSHRRXT---QAA-------------------HWNEEN" + "YRHYIAAFQHYTKXVSKQVDSVLKALYSTPAGRNTIVVIXADHGDGXA--" + "---------------SHRXVTKHISFYDEXTNVPFIFAG-PGIKQQKKPV" + "DHLLTQPTLDLLPTLCDLAGIA--VPAEKAGISLAPTLRGEKQKKSHPYV" + "VSEWHSEYEYVT-------------------------TPGRXVRGPRYKY" + "THYLE----------------------------GNGEELYDXKKDPGERK" + "NLAKDPKYSKILAEHRALLDDYITRSKDDY", ] ) def test_filename_selection(self): self.assertEqual( bioinformatics.alignment_parser_for( "dummy.pir" ), bioinformatics.pir_alignment_parse ) self.assertEqual( bioinformatics.alignment_parser_for( "clustal" ), None ) def test_known_formats(self): self.assertEqual( sorted( bioinformatics.known_alignment_formats() ), [ ".ali", ".aln", ".clustal", ".fa", ".fasta", ".hhr", ".pir" ] ) hhsearchout = \ """ Query Thu_Sep_09_20:47:04_+0200_2010 Match_columns 205 No_of_seqs 280 out of 1436 Neff 7.1 Searched_HMMs 22773 Date Thu Sep 9 20:51:32 2010 Command /cluster/toolkit/production/bioprogs/hhpred/hhsearch -cpu 4 -v 1 -i /cluster/toolkit/production/tmp/production/426773/3338418.hhm -d /cluster/toolkit/production/databases/hhpred/new_dbs/pdb70_9Sep10/db/pdb.hhm -o /cluster/toolkit/production/tmp/production/426773/3338418.hhr -p 20 -P 20 -Z 100 -B 100 -seq 1 -aliw 80 -local -ssm 2 -norealign -sc 1 -dbstrlen 10000 -cs /cluster/toolkit/production/bioprogs/csblast/data/clusters.prf No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 3cng_A Nudix hydrolase; struct 100.0 4.5E-28 2E-32 196.5 15.7 139 59-204 27-172 (189) 2 3i7u_A AP4A hydrolase; nudix p 99.9 1.4E-27 6.2E-32 182.2 13.1 127 69-196 4-130 (134) No 1 >3cng_A Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718} Probab=99.96 E-value=4.5e-28 Score=196.52 Aligned_cols=139 Identities=21% Similarity=0.317 Sum_probs=0.0 Q ss_pred hccCCC---CCceEEEEEEEEEECCEEEEEEcCC----CEEECCceeeCCCCCHHHHHHHHHHHHhCCccccceEEEEEe Q Thu_Sep_09_20: 59 FCNETG---YQTPKLDTRAAIFQEDKILLVQEND----GLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILD 131 (205) Q Consensus 59 ~~~~~g---y~Tpkv~v~a~v~~d~kiLLv~~~~----g~W~lPGG~ve~gEs~~eaa~REv~EETGl~v~~~~ll~v~~ 131 (205) |+.|| |+.|++.|.++|.++++|||++|+. |.|+||||++|.|||+++||+||++||||+++....+++++. T Consensus 27 ~C~~C~~~~y~~P~v~v~~ii~~~~~vLLv~r~~~~~~g~W~lPGG~ve~GEs~e~aa~REv~EEtGl~v~~~~l~~~~~ 106 (189) T 3cng_A 27 ICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYS 106 (189) T ss_dssp EETTTTEEECCCCEEEEEEEEEETTEEEEEEESSSSSTTCEECSEEECCTTCCHHHHHHHHHHHHHCCCEEEEEEEEEEE T ss_pred eCCCCCCcccCCCceEEEEEeecCceEEEEeccCCCCCCCEeCCcccCcCCCCHHHHHHHHHHhhhceeeeeeEEEEEee Q ss_pred eccccCCCCceEEEEEEEEEEecCCccCCCCCeEeEEEEcHHHCccccccCCCHHHHHHHHHHHhCCCCCCCc Q Thu_Sep_09_20: 132 KHKNNPAKSAHRVTKVFILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRF 204 (205) Q Consensus 132 ~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~E~~e~~Wf~~deLp~Ls~~r~~~~~i~~~f~~~r~~~~~t~f 204 (205) .... +...++|.|...++.+.++.|+.+++||++++||...+.-....+.-+.|...+..+....+ T Consensus 107 ~~~~-------~~~~~~f~~~~~~~~~~~~~E~~e~~wf~~~elp~~~la~~~~~~~l~~~~~~~~~g~~~~~ 172 (189) T 3cng_A 107 LPHI-------SQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFH 172 (189) T ss_dssp EGGG-------TEEEEEEEEEECCSCCCCCTTEEEEEEECTTTCCGGGBSCHHHHHHHHHHHHHHHHSSCCCE T ss_pred cccc-------ceeEEEEEEEeccCcccCcccceeEEEEcHHHCCchhcCcHHHHHHHHHHHHHhhcCCCccc No 2 >3i7u_A AP4A hydrolase; nudix protein, diadenosine polyphosphate, structural genomics, NPPSFA; HET: PGE; 1.80A {Aquifex aeolicus} PDB: 2pq1_A* 3i7u_A* 3i7v_A* Probab=99.95 E-value=1.4e-27 Score=182.17 Aligned_cols=127 Identities=20% Similarity=0.336 Sum_probs=0.0 Q ss_pred EEEEEEEEEECCEEEEEEcCCCEEECCceeeCCCCCHHHHHHHHHHHHhCCccccceEEEEEeeccccCCCCceEEEEEE Q Thu_Sep_09_20: 69 KLDTRAAIFQEDKILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKVF 148 (205) Q Consensus 69 kv~v~a~v~~d~kiLLv~~~~g~W~lPGG~ve~gEs~~eaa~REv~EETGl~v~~~~ll~v~~~~~~~~~~~~~~~~~~~ 148 (205) ++.++|+|+++|+|||+++.+|.|++|||++|.|||+.+||+||++||||+++....+++..+.. +.......+...++ T Consensus 4 ~~aAg~vv~~~~~vLlv~r~~~~w~~PgG~ve~gEt~~~aa~RE~~EEtGl~~~~~~~~~~~~~~-~~~~~~~~~~~~~~ 82 (134) T 3i7u_A 4 EFSAGGVLFKDGEVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEETGVKGEILDYIGEIHYW-YTLKGERIFKTVKY 82 (134) T ss_dssp EEEEEEEEEETTEEEEEECTTSCEECCEEECCTTCCHHHHHHHHHHHHHSEEEEEEEEEEEEEEE-EEETTEEEEEEEEE T ss_pred EEEEEEEEEECCEEEEEEeCCCcEECceeEeCCCCCHHHHHHhhhhheeceeEEEeeeeeeeeee-ccCCCceEEEEEEE Q ss_pred EEEEecCCccCCCCCeEeEEEEcHHHCccccccCCCHHHHHHHHHHHh Q Thu_Sep_09_20: 149 ILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASR 196 (205) Q Consensus 149 f~~~~~~~~~~~~~E~~e~~Wf~~deLp~Ls~~r~~~~~i~~~f~~~r 196 (205) |.+...++++.++.|+.+++|+++++++++....+....|..+++..+ T Consensus 83 f~~~~~~~~~~~~~E~~~~~W~~~~e~~~~l~~~~~r~il~~~~~l~~ 130 (134) T 3i7u_A 83 YLMKYKEGEPRPSWEVKDAKFFPIKEAKKLLKYKGDKEIFEKALKLKE 130 (134) T ss_dssp EEEEEEEECCCCCTTSSEEEEEEHHHHHHHCCSHHHHHHHHHHHHHHH T ss_pred EEEeccCCcccCChhheEEEEEeHHHHHhhcCChHHHHHHHHHHHHHh Done! """ hhalignout = """ Query 1XVQ.pdb Match_columns 155 No_of_seqs 111 out of 3723 Neff 9.0 Searched_HMMs 0 Date Tue Jul 13 19:50:02 2010 Command /work/dimaio/sequence/hhsearch/hhalign -i 1XVQ.hhm -t 1FOH.hhm -glob -o 1FOH_1XVQ.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 1FOH_aln.pdb 1.0 1 1 56.1 11.5 141 1-155 460-631 (649) No 1 >1FOH_aln.pdb Probab=1.00 E-value=1 Score=56.09 Aligned_columns=141 Identities=11% Q ss_pred CCCCCCCCCCCCCCEEEEC-CCCCEEEHHH-HC--CCEEEEEEECCCCCCCHHHHHHHHHHHHHHC-------------- Q ss_conf 9988554688178517897-9997764889-69--9848999832437711126669999998420-------------- Q 1XVQ.pdb 1 TVGELPAVGSPAPAFTLTG-GDLGVISSDQ-FR--GKSVLLNIFPSVDTPVCATSVRTFDERAAAS-------------- 62 (155) Q Consensus 1 ~~~~~p~vG~~aPdF~l~~-~~G~~v~ls~-~~--Gk~vvl~f~~~~~~p~c~~~~~~l~~~~~~~-------------- 62 (155) -...-+.+|..+|+.-+.. .+|....+.+ +. |++.++.|......+.-...+..+.+................... T Consensus 460 ~~~~~~~~G~r~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 539 (649) T 1FOH_aln.pdb 460 ELAKNCVVGTRFKSQPVVRHSEGLWMHFGDRLVTDGRFRIIVFAGKATDATQMSRIKKFSAYLDSENSVISLYTPKVSDR 539 (649) T ss_pred CCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCC T ss_conf 33688888864688503532788831125541278837999943888761135678888875204563011022466766 Q ss_pred --CEEECCCCCCCHH-----HHHHHHHHHCCCC------EEECCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCEE Q ss_conf --1000023467889-----9999999828975------11014433488997077344565557101279998699839 Q 1XVQ.pdb 63 --GATVLCVSKDLPF-----AQKRFCGAEGTEN------VMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNV 129 (155) Q Consensus 63 --g~~v~~i~~~~~~-----~~~~~~~~~~~~~------~~~~~d~~~~~~~~~g~~~~~~~~~~~~~p~~fiID~~G~I 129 (155) .+.++.|...... ............. .....|........||+..+ ..+.+||=|||-| T Consensus 540 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~g~~~~--------~~~~vlVRPD~~V 611 (649) T 1FOH_aln.pdb 540 NSRIDVITIHSCHRDDIEMHDFPAPALHPKWQYDFIYADCDSWHHPHPKSYQAWGVDET--------KGAVVVVRPDGYT 611 (649) T ss_pred CCCEEEEEEECCCCCCCCHHHCHHHHCCCCCCCEEEEECCCCCCCCCHHHHHHHCCCHH--------CCEEEEECCCCEE T ss_conf 56168999854776544233320200246742016650444444667789998098711--------4379998699558 Q ss_pred EEEEECCCCCCCCCHHHHHHHHHHHC Q ss_conf 99998178888889999999998519 Q 1XVQ.pdb 130 AYTELVPEIAQEPNYEAALAALGATS 155 (155) Q Consensus 130 ~~~~~~~~~~~~~~~~~il~~lkal~ 155 (155) .++. + .-+.+++.+.+...= T Consensus 612 a~~~--~----~~~~~~l~~~~~~~l 631 (649) T 1FOH_aln.pdb 612 SLVT--D----LEGTAEIDRYFSGIL 631 (649) T ss_pred EEEE--C----HHHHHHHHHHHHHHC T ss_conf 9997--3----013589999999742 Done! """ class test_hhsearch_parser(unittest.TestCase): def setUp(self): self.hss = bioinformatics.hhsearch_parser( output = hhsearchout ) def test_process_header(self): self.assertEqual( self.hss.query, "Thu_Sep_09_20:47:04_+0200_2010" ) self.assertEqual( self.hss.match_columns, 205 ) self.assertEqual( self.hss.no_of_sequences, ( 280, 1436 ) ) self.assertEqual( self.hss.neff, "7.1" ) self.assertEqual( self.hss.searched_hmms, 22773 ) self.assertEqual( self.hss.date, "Thu Sep 9 20:51:32 2010" ) self.assertEqual( self.hss.command, "/cluster/toolkit/production/bioprogs/hhpred/hhsearch -cpu 4 -v 1 -i /cluster/toolkit/production/tmp/production/426773/3338418.hhm -d /cluster/toolkit/production/databases/hhpred/new_dbs/pdb70_9Sep10/db/pdb.hhm -o /cluster/toolkit/production/tmp/production/426773/3338418.hhr -p 20 -P 20 -Z 100 -B 100 -seq 1 -aliw 80 -local -ssm 2 -norealign -sc 1 -dbstrlen 10000 -cs /cluster/toolkit/production/bioprogs/csblast/data/clusters.prf" ) def test_process_hits(self): self.assertEqual( self.hss.indices, [ 1, 2 ] ) self.assertEqual( self.hss.pdbs, [ "3CNG", "3I7U" ] ) self.assertEqual( self.hss.chains, [ "A", "A" ] ) self.assertEqual( self.hss.annotations, [ "Nudix hydrolase; structural genomics, APC7497, PSI-2, protein structure initiative, midwest center for structural genomics; 2.00A {Nitrosomonas europaea atcc 19718}", "AP4A hydrolase; nudix protein, diadenosine polyphosphate, structural genomics, NPPSFA; HET: PGE; 1.80A {Aquifex aeolicus} PDB: 2pq1_A* 3i7u_A* 3i7v_A*", ] ) self.assertIterablesAlmostEqual( self.hss.probabs, [ 99.96, 99.95 ], 2 ) self.assertIterablesAlmostEqual( self.hss.e_values, [ 4.5e-28, 1.4e-27 ], 28 ) self.assertIterablesAlmostEqual( self.hss.scores, [ 196.52, 182.17 ], 2 ) self.assertEqual( self.hss.aligned_cols, [ 139, 127 ] ) self.assertIterablesAlmostEqual( self.hss.identities, [ 21, 20 ], 1 ) self.assertEqual( self.hss.query_starts, [ 59, 69 ] ) self.assertEqual( self.hss.query_ends, [ 204, 196 ] ) self.assertEqual( self.hss.query_others, [ 205, 205 ] ) self.assertEqual( self.hss.query_alignments, [ "FCNETG---YQTPKLDTRAAIFQEDKILLVQEND----GLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILD" + "KHKNNPAKSAHRVTKVFILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASRSEHWETRF", "KLDTRAAIFQEDKILLVQENDGLWSLPGGWCDVDQSVKDNVVKEVKEEAGLDVEAQRVVAILDKHKNNPAKSAHRVTKVF" + "ILCRLLGGEFQPNSETVASGFFSLDDLPPLYLGKNTAEQLALCLEASR", ] ) self.assertEqual( self.hss.hit_starts, [ 27, 4 ] ) self.assertEqual( self.hss.hit_ends, [ 172, 130 ] ) self.assertEqual( self.hss.hit_others, [ 189, 134 ] ) self.assertEqual( self.hss.hit_alignments, [ "ICPKCHTIHYQNPKVIVGCIPEWENKVLLCKRAIAPYRGKWTLPAGFMENNETLVQGAARETLEEANARVEIRELYAVYS" + "LPHI-------SQVYMLFRAKLLDLDFFPGIESLEVRLFGEQEIPWNDIAFRVIHDPLKRYMEERHHGQPAFH", "EFSAGGVLFKDGEVLLIKTPSNVWSFPKGNIEPGEKPEETAVREVWEETGVKGEILDYIGEIHYW-YTLKGERIFKTVKY" + "YLMKYKEGEPRPSWEVKDAKFFPIKEAKKLLKYKGDKEIFEKALKLKE", ] ) def assertIterablesAlmostEqual(self, i1, i2, digits): self.assertEqual( len( i1 ), len( i2 ) ) for ( o, e ) in zip( i1, i2 ): self.assertAlmostEqual( o, e, digits ) class test_hhalign_parser(unittest.TestCase): def setUp(self): self.hss = bioinformatics.hhalign_parser( output = hhalignout ) def test_process_header(self): self.assertEqual( self.hss.query, "1XVQ.pdb" ) self.assertEqual( self.hss.match_columns, 155 ) self.assertEqual( self.hss.no_of_sequences, ( 111, 3723 ) ) self.assertEqual( self.hss.neff, "9.0" ) self.assertEqual( self.hss.searched_hmms, 0 ) self.assertEqual( self.hss.date, "Tue Jul 13 19:50:02 2010" ) self.assertEqual( self.hss.command, "/work/dimaio/sequence/hhsearch/hhalign -i 1XVQ.hhm -t 1FOH.hhm -glob -o 1FOH_1XVQ.hhr" ) def test_process_hits(self): self.assertEqual( self.hss.indices, [ 1 ] ) self.assertEqual( self.hss.annotations, [ "1FOH_aln.pdb" ] ) self.assertIterablesAlmostEqual( self.hss.probabs, [ 1.0 ], 2 ) self.assertIterablesAlmostEqual( self.hss.e_values, [ 1.0 ], 2 ) self.assertIterablesAlmostEqual( self.hss.scores, [ 56.09 ], 2 ) self.assertEqual( self.hss.aligned_cols, [ 141 ] ) self.assertIterablesAlmostEqual( self.hss.identities, [ 11 ], 1 ) self.assertEqual( self.hss.query_starts, [ 1 ] ) self.assertEqual( self.hss.query_ends, [ 155 ] ) self.assertEqual( self.hss.query_others, [ 155 ] ) self.assertEqual( self.hss.query_alignments, [ "TVGELPAVGSPAPAFTLTG-GDLGVISSDQ-FR--GKSVLLNIFPSVDTPVCATSVRTFDERAAAS--------------" + "--GATVLCVSKDLPF-----AQKRFCGAEGTEN------VMPASAFRDSFGEDYGVTIADGPMAGLLARAIVVIGADGNV" + "AYTELVPEIAQEPNYEAALAALGATS", ] ) self.assertEqual( self.hss.query_consensi, [ "~~~~~p~vG~~aPdF~l~~-~~G~~v~ls~-~~--Gk~vvl~f~~~~~~p~c~~~~~~l~~~~~~~--------------" + "--g~~v~~i~~~~~~-----~~~~~~~~~~~~~------~~~~~d~~~~~~~~~g~~~~~~~~~~~~~p~~fiID~~G~I" + "~~~~~~~~~~~~~~~~~il~~lkal~", ] ) self.assertEqual( self.hss.query_ss_preds, [ "CCCCCCCCCCCCCCEEEEC-CCCCEEEHHH-HC--CCEEEEEEECCCCCCCHHHHHHHHHHHHHHC--------------" + "--CEEECCCCCCCHH-----HHHHHHHHHCCCC------EEECCCCCHHHHHHCCCCCCCCCCCCCEEEEEEEECCCCEE" + "EEEEECCCCCCCCCHHHHHHHHHHHC", ] ) self.assertEqual( self.hss.query_ss_confs, [ "9988554688178517897-9997764889-69--9848999832437711126669999998420--------------" + "--1000023467889-----9999999828975------11014433488997077344565557101279998699839" + "99998178888889999999998519", ] ) self.assertEqual( self.hss.midlines, [ "-...-+.+|..+|+.-+.. .+|....+.+ +. |++.++.|......+.-...+..+.+..................." + " .+.++.|...... ............. .....|........||+..+ ..+.+||=|||-|" + ".++. + .-+.+++.+.+...=", ] ) self.assertEqual( self.hss.hit_starts, [ 460 ] ) self.assertEqual( self.hss.hit_ends, [ 631 ] ) self.assertEqual( self.hss.hit_others, [ 649 ] ) self.assertEqual( self.hss.hit_ss_preds, [ "CCCCCCCCCCCCCCCCEEECCCCCCCCHHHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCC" + "CCCEEEEEEECCCCCCCCHHHCHHHHCCCCCCCEEEEECCCCCCCCCHHHHHHHCCCHH--------CCEEEEECCCCEE" + "EEEE--C----HHHHHHHHHHHHHHC", ] ) self.assertEqual( self.hss.hit_ss_confs, [ "33688888864688503532788831125541278837999943888761135678888875204563011022466766" + "56168999854776544233320200246742016650444444667789998098711--------4379998699558" + "9997--3----013589999999742", ] ) self.assertEqual( self.hss.hit_consensi, [ "~~~~~~~~G~r~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + "~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~g~~~~--------~~~~vlVRPD~~V" + "a~~~--~----~~~~~~l~~~~~~~l", ] ) self.assertEqual( self.hss.hit_alignments, [ "ELAKNCVVGTRFKSQPVVRHSEGLWMHFGDRLVTDGRFRIIVFAGKATDATQMSRIKKFSAYLDSENSVISLYTPKVSDR" + "NSRIDVITIHSCHRDDIEMHDFPAPALHPKWQYDFIYADCDSWHHPHPKSYQAWGVDET--------KGAVVVVRPDGYT" + "SLVT--D----LEGTAEIDRYFSGIL", ] ) def assertIterablesAlmostEqual(self, i1, i2, digits): self.assertEqual( len( i1 ), len( i2 ) ) for ( o, e ) in zip( i1, i2 ): self.assertAlmostEqual( o, e, digits ) def exercise_guess_chain_types(): from iotbx.bioinformatics import \ guess_chain_types_from_sequences,text_from_chains_matching_chain_type print("Testing guess_chain_types ...", end=' ') text_rna=""" >4a17.pdb|Chain=2 AGAAAAUUUUCAACGGUGGAUAUCUAGGUUCCCGUGACGAUGAAGAACGCAGCGAAAUGCGAUACGCAAUGCGAAUUGCA GAACCGCGAGUCAUCAGAUCUUUGAACGCAAGUGGUGGAGGUGUAAAAACCUUCAUGUUUGUUUCAGUGUGGAA """ text_ambiguous=""" >4a17.pdb|Chain=A TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT """ text_ambiguous_a=""" >4a17.pdb|Chain=A AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA """ text_ambiguous_ag=""" AAAAAAAG """ text_protein=""" >4a17.pdb|Chain=A GRVIRAQRKGRANGVYKSHKSGRIAPAQYRVYDFAERQGYIRGCIRDIVHEPGRGAPLAEVAFRDPYRYKTNKEHFIAAE GQYSGQYVYCGLKAQIAVGNVLPINRIPEGTVVCNVEEKVGDRGTFSRASGCYATIIGHSEDGDKTRIRLPSGARKTIPG SCRATVGIVAGGGRTDKPILKAGNQFHKYARKRKSWPRVRGVAMNPVDHPHGGGNHQHIGHPATVSKWASAGQKVGLRAA RRTGLVRGGQKEKMAMK """ text_dna=""" >4a17.pdb|Chain=B GATCCCTTTCCC """ text_misc=""" UGGAGAGUUUGAUCCU asdfaafasdfafsdea """ text_misc_2=""" >> chain 1 UGGAGAGUUUGAUCCU >> chain 2 asdfaafasdfafsdea """ text_misc_3=""" >> chain 1 UGGAGAGUUUGAUCCU >> chain 2 """ text_protein_pdb = \ """ ATOM 2 CA GLY A 511 12.652 44.232 24.646 1.00 31.14 A C ATOM 6 CA ASP A 512 9.025 45.287 24.299 1.00 36.73 A C ATOM 14 CA PRO A 513 7.666 41.856 25.348 1.00 32.96 A C ATOM 21 CA VAL A 514 9.071 42.422 28.848 1.00 29.77 A C ATOM 28 CA THR A 515 6.954 45.559 29.147 1.00 33.07 A C ATOM 35 CA ARG A 516 3.960 43.821 27.518 1.00 36.02 A C ATOM 46 CA VAL A 517 4.094 40.967 30.053 1.00 29.54 A C ATOM 53 CA LEU A 518 4.292 43.291 33.052 1.00 27.54 A C ATOM 61 CA ASP A 519 1.537 45.543 31.676 1.00 29.63 A C ATOM 69 CA ASP A 520 -0.827 42.633 30.996 1.00 31.79 A C """ text_rna_pdb = \ """ ATOM 23 P G U 1 13.063 22.026 11.420 1.00 0.00 ATOM 43 P U U 2 18.716 21.164 10.071 1.00 0.00 ATOM 66 P G U 3 22.765 18.088 7.789 1.00 0.00 ATOM 89 P G U 4 23.803 13.287 4.325 1.00 0.00 ATOM 109 P U U 5 21.549 8.522 0.878 1.00 0.00 ATOM 132 P G U 6 18.176 5.108 -2.281 1.00 0.00 ATOM 160 P A V 2 5.037 12.654 6.095 1.00 0.00 ATOM 180 P C V 3 6.536 7.470 8.349 1.00 0.00 ATOM 200 P C V 4 10.409 4.550 10.972 1.00 0.00 ATOM 222 P A V 5 15.160 3.698 14.124 1.00 0.00 ATOM 242 P C V 6 19.171 5.322 17.832 1.00 0.00 """ text_rna_pdb_o_two = \ """ ATOM 23 P G U 1 13.063 22.026 11.420 1.00 0.00 ATOM 24 O2' G U 1 14.063 23.026 12.420 1.00 0.00 ATOM 43 P U U 2 18.716 21.164 10.071 1.00 0.00 ATOM 66 P G U 3 22.765 18.088 7.789 1.00 0.00 ATOM 89 P G U 4 23.803 13.287 4.325 1.00 0.00 ATOM 109 P U U 5 21.549 8.522 0.878 1.00 0.00 ATOM 132 P G U 6 18.176 5.108 -2.281 1.00 0.00 ATOM 160 P A V 2 5.037 12.654 6.095 1.00 0.00 ATOM 180 P C V 3 6.536 7.470 8.349 1.00 0.00 ATOM 200 P C V 4 10.409 4.550 10.972 1.00 0.00 ATOM 222 P A V 5 15.160 3.698 14.124 1.00 0.00 ATOM 242 P C V 6 19.171 5.322 17.832 1.00 0.00 """ text_dna_pdb = \ """ ATOM 23 P G U 1 13.063 22.026 11.420 1.00 0.00 ATOM 43 P T U 2 18.716 21.164 10.071 1.00 0.00 ATOM 66 P G U 3 22.765 18.088 7.789 1.00 0.00 ATOM 89 P G U 4 23.803 13.287 4.325 1.00 0.00 ATOM 109 P T U 5 21.549 8.522 0.878 1.00 0.00 ATOM 132 P G U 6 18.176 5.108 -2.281 1.00 0.00 ATOM 160 P A V 2 5.037 12.654 6.095 1.00 0.00 ATOM 180 P C V 3 6.536 7.470 8.349 1.00 0.00 ATOM 200 P C V 4 10.409 4.550 10.972 1.00 0.00 ATOM 222 P A V 5 15.160 3.698 14.124 1.00 0.00 ATOM 242 P C V 6 19.171 5.322 17.832 1.00 0.00 """ text_dna_pdb_lc = \ """ ATOM 23 P g U 1 13.063 22.026 11.420 1.00 0.00 ATOM 43 P t U 2 18.716 21.164 10.071 1.00 0.00 ATOM 66 P g U 3 22.765 18.088 7.789 1.00 0.00 ATOM 89 P g U 4 23.803 13.287 4.325 1.00 0.00 ATOM 109 P t U 5 21.549 8.522 0.878 1.00 0.00 ATOM 132 P g U 6 18.176 5.108 -2.281 1.00 0.00 ATOM 160 P a V 2 5.037 12.654 6.095 1.00 0.00 ATOM 180 P c V 3 6.536 7.470 8.349 1.00 0.00 ATOM 200 P c V 4 10.409 4.550 10.972 1.00 0.00 ATOM 222 P a V 5 15.160 3.698 14.124 1.00 0.00 ATOM 242 P c V 6 19.171 5.322 17.832 1.00 0.00 """ assert guess_chain_types_from_sequences(text=text_protein)==["PROTEIN"] assert guess_chain_types_from_sequences(text=text_dna)==["DNA"] assert guess_chain_types_from_sequences(text=text_rna)==["RNA"] assert guess_chain_types_from_sequences( text=text_protein+text_rna)==["PROTEIN","RNA"] assert guess_chain_types_from_sequences( text=text_protein+text_dna)==["DNA","PROTEIN"] assert guess_chain_types_from_sequences( text=text_rna+text_protein+text_dna)==["DNA","PROTEIN","RNA"] assert guess_chain_types_from_sequences( text=text_rna+text_dna)==["DNA","RNA"] assert guess_chain_types_from_sequences(text="XX")==[] assert guess_chain_types_from_sequences(text=text_misc)==["PROTEIN","RNA"] assert guess_chain_types_from_sequences(text=text_misc_2)==["PROTEIN","RNA"] assert guess_chain_types_from_sequences(text=text_misc_3)==["RNA"] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_misc_2))==["PROTEIN","RNA"] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_misc_3))==["RNA"] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_protein))==["PROTEIN"] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_ambiguous))==['DNA'] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_ambiguous_a))==['PROTEIN'] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_ambiguous_ag))==['PROTEIN'] assert guess_chain_types_from_sequences(text= text_from_chains_matching_chain_type(text=text_ambiguous_a), likely_chain_types=['RNA'])==['RNA'] assert guess_chain_types_from_sequences(text=text_ambiguous, likely_chain_types=['PROTEIN','RNA']) == ['PROTEIN'] assert text_from_chains_matching_chain_type( text=text_ambiguous,chain_type='PROTEIN')==""" > TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT """ print("OK") def exercise_random_sequences(): import random random.seed(71231) seq=bioinformatics.random_sequence(n_residues=100, residue_basket=residue_basket) # random number generator is not consistent between Python 2 and 3 assert len(seq) == 100 assert seq.count('E') > seq.count('D') assert seq.count('D') > seq.count('C') assert seq.count('C') > seq.count('A') seq=bioinformatics.random_sequence(n_residues=100, chain_type = 'PROTEIN') assert len(seq) == 100 seq=bioinformatics.random_sequence(n_residues=100, chain_type = 'RNA') assert len(seq) == 100 seq=bioinformatics.random_sequence(n_residues=100, chain_type = 'DNA') assert len(seq) == 100 seq=bioinformatics.random_sequence(n_residues=100) assert len(seq) == 100 def exercise_merge_sequences(): print("Testing merge_sequences ...", end=' ') with open("tmp_iotbx_bioinfo.fa", "w") as f: f.write("""\ > 9zzz ARGLYS > 8xxx PHETYR""") output_file = "tmp_iotbx_bioinfo_merged.fa" bioinformatics.merge_sequence_files( file_names=["tmp_iotbx_bioinfo.fa"], output_file=output_file, sequences=["SERTHR"]) seq_in, nc = bioinformatics.any_sequence_format(output_file) assert (len(seq_in) == 3) and (len(nc) == 0) print("OK") suite_sequence = unittest.TestLoader().loadTestsFromTestCase( test_sequence ) suite_fasta_sequence = unittest.TestLoader().loadTestsFromTestCase( test_fasta_sequence ) suite_pir_sequence = unittest.TestLoader().loadTestsFromTestCase( test_pir_sequence ) suite_midline = unittest.TestLoader().loadTestsFromTestCase( test_midline ) suite_alignment = unittest.TestLoader().loadTestsFromTestCase( test_alignment ) suite_fasta_alignment = unittest.TestLoader().loadTestsFromTestCase( test_fasta_alignment ) suite_pir_alignment = unittest.TestLoader().loadTestsFromTestCase( test_pir_alignment ) suite_clustal_alignment = unittest.TestLoader().loadTestsFromTestCase( test_clustal_alignment ) suite_sequence_parse = unittest.TestLoader().loadTestsFromTestCase( test_sequence_parse ) suite_alignment_parse = unittest.TestLoader().loadTestsFromTestCase( test_alignment_parse ) suite_hhsearch_parser = unittest.TestLoader().loadTestsFromTestCase( test_hhsearch_parser ) suite_hhalign_parser = unittest.TestLoader().loadTestsFromTestCase( test_hhalign_parser ) alltests = unittest.TestSuite( [ suite_sequence, suite_fasta_sequence, suite_pir_sequence, suite_midline, suite_alignment, suite_fasta_alignment, suite_pir_alignment, suite_clustal_alignment, suite_sequence_parse, suite_alignment_parse, suite_hhsearch_parser, suite_hhalign_parser, ] ) if __name__ == "__main__": exercise_guess_chain_types() exercise_merge_sequences() exercise_random_sequences() unittest.TextTestRunner( stream=sys.stdout, verbosity = 2 ).run( alltests )