def test_get_percentage_identity():
alignment = BlastAlignment('pdb|1crn|A', 'AVAVAVAVAV', '',
1, 10, 'AVAVAVAVAV',
1, 10, 'ATATATATAT')
eq_(alignment.get_percentage_identity(), 50.0)
alignment = TargetTemplateAlignment('AVAVAVAVAV',
'ATATATATAT')
eq_(alignment.get_percentage_identity(), 50.0)
def test_count_aligned_residues():
alignment = BlastAlignment('pdb|1crn|A', 'AVAVAVAVAV', '',
1, 10, 'AVAVAVAVAV',
1, 10, 'A-A-A-A-A-')
eq_(alignment.count_aligned_residues(), 5)
alignment = TargetTemplateAlignment('AVAVAVAVAV',
'A-A-A-A-A-')
eq_(alignment.count_aligned_residues(), 5)
def test_get_percentage_coverage():
alignment = BlastAlignment('pdb|1crn|A', 'AVAVAVAVAV', '',
1, 10, 'AVAVAVAVAV',
1, 10, 'A-A-A-A-A-')
eq_(alignment.get_percentage_coverage(), 50.0)
alignment = TargetTemplateAlignment('AVAVAVAVAV',
'A-A-A-A-A-')
eq_(alignment.get_percentage_coverage(), 50.0)
def test_get_query_range():
full_sequence = """
MSSSHSRAGQSAAGAAPGGGVDTRDAEMPATEKDLAEDAPWKKIQQNTFTRWCNEHLKCVSKRIANLQTDLS
DGLRLIALLEVLSQKKMHRKHNQRPTFRQMQLENVSVALEFLDRESIKLVSIDSKAIVDGNLKLILGLIWTL
ILHYSISMPMWDEEEDEEAKKQTPKQRLLGWIQNKLPQLPITNFSRDWQSGRALGALVDSCAPGLCPDWDSW
DASKPVTNAREAMQQADDWLGIPQVITPEEIVDPNVDEHSVMTYLSQFPKAKLKPGAPLRPKLNPKKARAYG
PGIEPTGNMVKKRAEFTVETRSAGQGEVLVYVEDPAGHQEEAKVTANNDKNRTFSVWYVPEVTGTHKVTVLF
AGQHIAKSPFEVYVDKSQGDASKVTAQGPGLEPSGNIANKTTYFEIFTAGAGTGEVEVVIQDPMGQKGTVEP
QLEARGDSTYRCSYQPTMEGVHTVHVTFAGVPIPRSPYTVTVGQACNPSACRAVGRGLQPKGVRVKETADFK
VYTKGAGSGELKVTVKGPKGEERVKQKDLGDGVYGFEYYPMVPGTYIVTITWGGQNIGRSPFEVKVGTECGN
QKVRAWGPGLEGGVVGKSADFVVEAIGDDVGTLGFSVEGPSQAKIECDDKGDGSCDVRYWPQEAGEYAVHVL
CNSEDIRLSPFMADIRDAPQDFHPDRVKARGPGLEKTGVAVNKPAEFTVDAKHGGKAPLRVQVQDNEGCPVE
ALVKDNGNGTYSCSYVPRKPVKHTAMVSWGGVSIPNSPFRVNVGAGSHPNKVKVYGPGVAKTGLKAHEPTYF
TVDCAEAGQGDVSIGIKCAPGVVGPAEADIDFDIIRNDNDTFTVKYTPRGAGSYTIMVLFADQATPTSPIRV
KVEPSHDASKVKAEGPGLSRTGVELGKPTHFTVNAKAAGKGKLDVQFSGLTKGDAVRDVDIIDHHDNTYTVK
YTPVQQGPVGVNVTYGGDPIPKSPFSVAVSPSLDLSKIKVSGLGEKVDVGKDQEFTVKSKGAGGQGKVASKI
VGPSGAAVPCKVEPGLGADNSVVRFLPREEGPYEVEVTYDGVPVPGSPFPLEAVAPTKPSKVKAFGPGLQGG
SAGSPARFTIDTKGAGTGGLGLTVEGPCEAQLECLDNGDGTCSVSYVPTEPGDYNINILFADTHIPGSPFKA
HVVPCFDASKVKCSGPGLERATAGEVGQFQVDCSSAGSAELTIEICSEAGLPAEVYIQDHGDGTHTITYIPL
CPGAYTVTIKYGGQPVPNFPSKLQVEPAVDTSGVQCYGPGIEGQGVFREATTEFSVDARALTQTGGPHVKAR
VANPSGNLTETYVQDRGDGMYKVEYTPYEEGLHSVDVTYDGSPVPSSPFQVPVTEGCDPSRVRVHGPGIQSG
TTNKPNKFTVETRGAGTGGLGLAVEGPSEAKMSCMDNKDGSCSVEYIPYEAGTYSLNVTYGGHQVPGSPFKV
PVHDVTDASKVKCSGPGLSPGMVRANLPQSFQVDTSKAGVAPLQVKVQGPKGLVEPVDVVDNADGTQTVNYV
PSREGPYSISVLYGDEEVPRSPFKVKVLPTHDASKVKASGPGLNTTGVPASLPVEFTIDAKDAGEGLLAVQI
TDPEGKPKKTHIQDNHDGTYTVAYVPDVTGRYTILIKYGGDEIPFSPYRVRAVPTGDASKCTVTVSIGGHGL
GAGIGPTIQIGEETVITVDTKAAGKGKVTCTVCTPDGSEVDVDVVENEDGTFDIFYTAPQPGKYVICVRFGG
EHVPNSPFQVTALAGDQPSVQPPLRSQQLAPQYTYAQGGQQTWAPERPLVGVNGLDVTSLRPFDLVIPFTIK
KGEITGEVRMPSGKVAQPTITDNKDGTVTVRYAPSEAGLHEMDIRYDNMHIPGSPLQFYVDYVNCGHVTAYG
PGLTHGVVNKPATFTVNTKDAGEGGLSLAIEGPSKAEISCTDNQDGTCSVSYLPVLPGDYSILVKYNEQHVP
GSPFTARVTGDDSMRMSHLKVGSAADIPINISETDLSLLTATVVPPSGREEPCLLKRLRNGHVGISFVPKET
GEHLVHVKKNGQHVASSPIPVVISQSEIGDASRVRVSGQGLHEGHTFEPAEFIIDTRDAGYGGLSLSIEGPS
KVDINTEDLEDGTCRVTYCPTEPGNYIINIKFADQHVPGSPFSVKVTGEGRVKESITRRRRAPSVANVGSHC
DLSLKIPEISIQDMTAQVTSPSGKTHEAEIVEGENHTYCIRFVPAEMGTHTVSVKYKGQHVPGSPFQFTVGP
LGEGGAHKVRAGGPGLERAEAGVPAEFSIWTREAGAGGLAIAVEGPSKAEISFEDRKDGSCGVAYVVQEPGD
YEVSVKFNEEHIPDSPFVVPVASPSGDARRLTVSSLQESGLKVNQPASFAVSLNGAKGAIDAKVHSPSGALE
ECYVTEIDQDKYAVRFIPRENGVYLIDVKFNGTHIPGSPFKIRVGEPGHGGDPGLVSAYGAGLEGGVTGNPA
EFVVNTSNAGAGALSVTIDGPSKVKMDCQECPEGYRVTYTPMAPGSYLISIKYGGPYHIGGSPFKAKVTGPR
LVSNHSLHETSSVFVDSLTKATCAPQHGAPGPGPADASKVVAKGLGLSKAYVGQKSSFTVDCSKAGNNMLLV
GVHGPRTPCEEILVKHVGSRLYSVSYLLKDKGEYTLVVKWGDEHIPGSPYRVVVP
""".replace('\n', '')
alignment = BlastAlignment('pdb|4M9P|A', full_sequence, 'pdb',
282, 475,
"KKARAYGPGIEPTGNMVKKRAEFTVETRSAGQGEVLVYVEDPAGHQEEAKVTANNDKNRT" +
"FSVWYVPEVTGTHKVTVLFAGQHIAKSPFEVYVDKSQGD--ASKVTAQGPGLEPSGNIAN" +
"KTTYFEIFTAGAGTGEVEVVIQDPMGQKGTVEPQLEARGDSTYRCSYQPTMEGVHTVHVT" +
"FAGVPIPRSPYTVTVG",
100, 287,
"QKVRAWGPGLE--GGVVGKSADFVVEAIGDDVGTLGFSVEGPS--Q--AKIECDDKGDGS" +
"CDVRYWPQEAGEYAVHVLCNSEDIRLSPFMADIRDAPQDFHPDRVKARGPGLEKTGVAVN" +
"KPAEFTVDAKHGGKAPLRVQVQDNEG--CPVEALVKDNGNGTYSCSYVPRKPVKHTAMVS" +
"WGGVSIPNSPFRVNVG")
r = alignment.get_query_range()
eq_(r.start, 281)
eq_(r.end, 475)
def test_is_better_than():
hit1 = BlastAlignment('', '', '', 1, 10, 'AAAAAAAAAA', 1, 10, 'AAAAAAAAAA')
hit2 = BlastAlignment('', '', '', 1, 10, 'AAAAAAAAAA', 1, 10, '-AAAAAAAAA')
ok_(domain_aligner._is_better_than(hit1, hit2))
ok_(not domain_aligner._is_better_than(hit2, hit1))
hit1 = BlastAlignment('', '', '', 1, 10, 'AAAAAAAAAA', 1, 10, 'AAAAAAAAAA')
hit2 = BlastAlignment('', '', '', 1, 10, 'AAAAAAAAAA', 1, 10, 'VAAAAAAAAA')
ok_(domain_aligner._is_better_than(hit1, hit2))
ok_(not domain_aligner._is_better_than(hit2, hit1))
def test_get_hit_type():
alignment = BlastAlignment('pdb|1crn|A', '', '', 0, 0, '', 0, 0, '')
eq_(alignment.get_hit_type(), 'pdb')
alignment = BlastAlignment('sp|P00395|COX1_HUMAN', '', '', 0, 0, '', 0, 0, '')
eq_(alignment.get_hit_type(), 'sp')
alignment = BlastAlignment('1crn_A', '', '', 0, 0, '', 0, 0, '')
eq_(alignment.get_hit_type(), 'pdb')
def _parse_alignments(self, xml_str, full_query_sequence, databank):
hits = {}
root = ET.fromstring(xml_str)
iterations = root.find('BlastOutput_iterations')
for it in iterations.findall('Iteration'):
for mem in it.findall('Iteration_hits'):
for hit in mem.findall('Hit'):
hit_id = hit.find('Hit_def').text
hits[hit_id] = []
hsps = hit.find('Hit_hsps')
for hsp in hsps.findall('Hsp'):
query_start = int(hsp.find('Hsp_query-from').text)
query_end = int(hsp.find('Hsp_query-to').text)
query_alignment = hsp.find('Hsp_qseq').text
subject_start = int(hsp.find('Hsp_hit-from').text)
subject_end = int(hsp.find('Hsp_hit-to').text)
subject_alignment = hsp.find('Hsp_hseq').text
hits[hit_id].append(
BlastAlignment(hit_id, full_query_sequence,
databank, query_start, query_end,
query_alignment, subject_start,
subject_end, subject_alignment))
return hits
def test_getters():
q = 'HALAILA'
s = 'WALALLA'
alignment = BlastAlignment('pdb|xxxx|X', q, '',
1, 7, q,
1, 7, s)
eq_(alignment.subject_alignment, s)
def test_conversion():
full_sequence = """
MKMASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAV
WIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGLLEYLSRISICKMKKDYRKKYRKYV
RSRFQCIEDRNARLGESVSLNKRYTRLRLIKEHRSQQEREQELLAIGKTKTCESPVSPIKMELLFDPDDEHS
EPVHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLFYIHCREVSLVTQRSLGDLIMSCCPDPNPPIH
KIVRKPSRILFLMDGFDELQGAFDEHIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQH
LLDHPRHVEILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESGKSL
AQTSKTTTAVYVFFLSSLLQPRGGSQEHGLCAHLWGLCSLAADGIWNQKILFEESDLRNHGLQKADVSAFLR
MNLFQKEVDCEKFYSFIHMTFQEFFAAMYYLLEEEKEGRTNVPGSRLKLPSRDVTVLLENYGKFEKGYLIFV
VRFLFGLVNQERTSYLEKKLSCKISQQIRLELLKWIEVKAKAKKLQIQPSQLELFYCLYEMQEEDFVQRAMD
YFPKIEINLSTRMDHMVSSFCIENCHRVESLSLGFLHNMPKEEEEEEKEGRHLDMVQCVLPSSSHAACSHGL
VNSHLTSSFCRGLFSVLSTSQSLTELDLSDNSLGDPGMRVLCETLQHPGCNIRRLWLGRCGLSHECCFDISL
VLSSNQKLVELDLSDNALGDFGIRLLCVGLKHLLCNLKKLWLVSCCLTSACCQDLASVLSTSHSLTRLYVGE
NALGDSGVAILCEKAKNPQCNLQKLGLVNSGLTSVCCSALSSVLSTNQNLTHLYLRGNTLGDKGIKLLCEGL
LHPDCKLQVLELDNCNLTSHCCWDLSTLLTSSQSLRKLSLGNNDLGDLGVMMFCEVLKQQSCLLQNLGLSEM
YFNYETKSALETLQEEKPELTVVFEPSW
""".replace('\n', '')
alignment = BlastAlignment('pdb|5IRM|C', full_sequence, 'pdb',
198, 452,
"SPVSPIKMELLFDPDDEHSEPVHTVVFQGAAGIGKTILARKMMLDWASGTLYQDRFDYLF" +
"YIHCREVSLVTQR-SLGDLIMS-CC-PDPNPP-IHK-IVRKPSRILFLMDGFDELQGAF-" +
"DE--HIGPLCTDWQKAERGDILLSSLIRKKLLPEASLLITTRPVALEKLQHLLDHPRHVE" +
"ILGFSEAKRKEYFFKYFSDEAQARAAFSLIQENEVLFTMCFIPLVCWIVCTGLKQQMESG" +
"KSLAQTSKTTTAVYVFFLSSLLQ",
1, 252,
"SPAA-LGLEELFSPNGHLNEDADTVLVVGEAGSGKSTLLQQVHLLWATGQDFQE-FLFVF" +
"PFSCRQLQCVARPLSVMTLLFEHCCWPDVGQQDVFQFLLDHPDRILLTFDGFDEFKFKFT" +
"DHERHCSP--TDPTSVQ---TLLFNLLQGNLLKNARKVLTSRPDAVSAF-LRKYVRTEFN" +
"LKGFSEEGIELYLRKCHREPGVADRLIHLLQTTSALHGLCHLPVFSWMV--S-KCHQELL" +
"LQDGGSPKTTTDMYLLILQHFLR")
range_ = alignment.get_query_range()
template_id = TemplateID('5IRM', 'C')
domain_alignment = DomainAlignment(alignment.query_alignment,
alignment.subject_alignment,
range_, template_id)
ok_(domain_alignment.is_target_residue_covered(317))
def test_get_hit_accession_code():
alignment = BlastAlignment('sp|P00395|COX1_HUMAN', '', '', 0, 0, '', 0, 0, '')
eq_(alignment.get_hit_accession_code(), 'P00395')
def test_get_hit_chain_id():
alignment = BlastAlignment('pdb|1crn|A', '', '', 0, 0, '', 0, 0, '')
eq_(alignment.get_hit_chain_id(), 'A')