# Copyright 2006-2014 by Peter Cock. All rights reserved. # Revisions copyright 2011 Brandon Invergo. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Bio.AlignIO.PhylipIO""" import unittest from Bio._py3k import StringIO from Bio.AlignIO.PhylipIO import PhylipIterator, PhylipWriter phylip_text = """ 8 286 V_Harveyi_ --MKNWIKVA VAAIA--LSA A--------- ---------T VQAATEVKVG B_subtilis MKMKKWTVLV VAALLAVLSA CG-------- ----NGNSSS KEDDNVLHVG B_subtilis MKKALLALFM VVSIAALAAC GAGNDNQSKD NAKDGDLWAS IKKKGVLTVG YA80_HAEIN MKKLLFTTAL LTGAIAFSTF ---------- -SHAGEIADR VEKTKTLLVG FLIY_ECOLI MKLAHLGRQA LMGVMAVALV AG---MSVKS FADEG-LLNK VKERGTLLVG E_coli_Gln --MKSVLKVS LAALTLAFAV S--------- ---------S HAADKKLVVA Deinococcu -MKKSLLSLK LSGLLVPSVL ALS------- -LSACSSPSS TLNQGTLKIA HISJ_E_COL MKKLVLSLSL VLAFSSATAA F--------- ---------- AAIPQNIRIG MSGRYFPFTF VKQ--DKLQG FEVDMWDEIG KRNDYKIEYV TANFSGLFGL ATGQSYPFAY KEN--GKLTG FDVEVMEAVA KKIDMKLDWK LLEFSGLMGE TEGTYEPFTY HDKDTDKLTG YDVEVITEVA KRLGLKVDFK ETQWGSMFAG TEGTYAPFTF HDK-SGKLTG FDVEVIRKVA EKLGLKVEFK ETQWDAMYAG LEGTYPPFSF QGD-DGKLTG FEVEFAQQLA KHLGVEASLK PTKWDGMLAS TDTAFVPFEF KQG--DKYVG FDVDLWAAIA KELKLDYELK PMDFSGIIPA MEGTYPPFTS KNE-QGELVG FDVDIAKAVA QKLNLKPEFV LTEWSGILAG TDPTYAPFES KNS-QGELVG FDIDLAKELC KRINTQCTFV ENPLDALIPS LETGRIDTIS NQITMTDARK AKYLFADPYV VDG-AQITVR KGNDSIQGVE LQTGKLDTIS NQVAVTDERK ETYNFTKPYA YAG-TQIVVK KDNTDIKSVD LNSKRFDVVA NQVG-KTDRE DKYDFSDKYT TSR-AVVVTK KDNNDIKSEA LNAKRFDVIA NQTNPSPERL KKYSFTTPYN YSG-GVIVTK SSDNSIKSFE LDSKRIDVVI NQVTISDERK KKYDFSTPYT ISGIQALVKK GNEGTIKTAD LQTKNVDLAL AGITITDERK KAIDFSDGYY KSG-LLVMVK ANNNDVKSVK LQANKYDVIV NQVGITPERQ NSIGFSQPYA YSRPEIIVAK NNTFNPQSLA LKAKKIDAIM SSLSITEKRQ QEIAFTDKLY AADSRLVVAK NSDIQP-TVE DLAGKTVAVN LGSNFEQLLR DYDKDGKINI KTYDT--GIE HDVALGRADA DLKGKTVAAV LGSNHAKNLE SKDPDKKINI KTYETQEGTL KDVAYGRVDA DVKGKTSAQS LTSNYNKLAT N----AGAKV EGVEGMAQAL QMIQQARVDM DLKGRKSAQS ATSNWGKDAK A----AGAQI LVVDGLAQSL ELIKQGRAEA DLKGKKVGVG LGTNYEEWLR QNV--QGVDV RTYDDDPTKY QDLRVGRIDA DLDGKVVAVK SGTGSVDYAK AN--IKTKDL RQFPNIDNAY MELGTNRADA DLKGKRVGST LGSNYEKQLI DTG---DIKI VTYPGAPEIL ADLVAGRIDA SLKGKRVGVL QGTTQETFGN EHWAPKGIEI VSYQGQDNIY SDLTAGRIDA FIMDRLSALE -LIKKT-GLP LQLAGEPFET I-----QNAW PFVDNEKGRK YVNSRTVLIA -QIKKT-GLP LKLAGDPIVY E-----QVAF PFAKDDAHDK TYNDKLAVLN -YLKTSGNKN VKIAFETGEP Q-----STYF TFRKGS--GE TINDKLAVLD -YFKQHPNSG LKIAYDRGDK T-----PTAF AFLQGE--DA ILVDRLAALD -LVKKT-NDT LAVTGEAFSR Q-----ESGV ALRKGN--ED VLHDTPNILY -FIKTAGNGQ FKAVGDSLEA Q-----QYGI AFPKGS--DE AYNDRLVVNY -IINDQ-KLP VRGAGQIGDA A-----PVGI ALKKGN--SA AFQDEVAASE GFLKQPVGKD YKFGGPSVKD EKLFGVGTGM GLRKED--NE LQAEVNKALA EMRADGTVEK ISVKWFGADI TK---- LRKKVNKALD ELRKDGTLKK LSEKYFNEDI TVEQKH VVDQVNKALK EMKEDGTLSK ISKKWFGEDV SK---- LITKFNQVLE ALRQDGTLKQ ISIEWFGYDI TQ---- LLKAVNDAIA EMQKDGTLQA LSEKWFGADV TK---- LRDKVNGALK TLRENGTYNE IYKKWFGTEP K----- LKDQIDKALT EMRSDGTFEK ISQKWFGQDV GQP--- LREALNKAFA EMRADGTYEK LAKKYFDFDV YGG--- """ # From here: # http://atgc.lirmm.fr/phyml/usersguide.html phylip_text2 = """5 60 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAG Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGG Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGG Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGG Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGG GAAATGGTCAATATTACAAGGT GAAATGGTCAACATTAAAAGAT GAAATCGTCAATATTAAAAGGT GAAATGGTCAATCTTAAAAGGT GAAATGGTCAATATTAAAAGGT""" phylip_text3 = """5 60 Tax1 CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT Tax2 CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT Tax3 CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT Tax4 TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT Tax5 CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT""" # From here: # http://evolution.genetics.washington.edu/phylip/doc/sequence.html # Note the lack of any white space between names 2 and 3 and their seqs. phylip_text4 = """ 5 42 Turkey AAGCTNGGGC ATTTCAGGGT Salmo gairAAGCCTTGGC AGTGCAGGGT H. SapiensACCGGTTGGC CGTTCAGGGT Chimp AAACCCTTGC CGTTACGCTT Gorilla AAACCCTTGC CGGTACGCTT GAGCCCGGGC AATACAGGGT AT GAGCCGTGGC CGGGCACGGT AT ACAGGTTGGC CGTTCAGGGT AA AAACCGAGGC CGGGACACTC AT AAACCATTGC CGGTACGCTT AA""" # From here: # http://evolution.genetics.washington.edu/phylip/doc/sequence.html phylip_text5 = """ 5 42 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA""" phylip_text5a = """ 5 42 Turkey AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA Chimp AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT Gorilla AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA""" class TestPhylipIO(unittest.TestCase): def test_one(self): handle = StringIO(phylip_text) ids = [] for alignment in PhylipIterator(handle): for record in alignment: ids.append(record.id) self.assertEqual(ids, ['V_Harveyi_', 'B_subtilis', 'B_subtilis', 'YA80_HAEIN', 'FLIY_ECOLI', 'E_coli_Gln', 'Deinococcu', 'HISJ_E_COL']) expected = """mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre alnkafaemradgtyeklak kyfdfdvygg""".replace(" ", "").replace("\n", "").upper() self.assertEqual(str(record.seq).replace("-", ""), expected) def test_two_and_three(self): handle = StringIO(phylip_text2) list2 = list(PhylipIterator(handle)) handle.close() self.assertEqual(len(list2), 1) self.assertEqual(len(list2[0]), 5) handle = StringIO(phylip_text3) list3 = list(PhylipIterator(handle)) handle.close() self.assertEqual(len(list3), 1) self.assertEqual(len(list3[0]), 5) for i in range(0, 5): self.assertEqual(list2[0][i].id, list3[0][i].id) self.assertEqual(str(list2[0][i].seq), str(list3[0][i].seq)) def test_four(self): handle = StringIO(phylip_text4) list4 = list(PhylipIterator(handle)) handle.close() self.assertEqual(len(list4), 1) self.assertEqual(len(list4[0]), 5) def test_five(self): handle = StringIO(phylip_text5) self.assertRaises(ValueError, list, PhylipIterator(handle)) handle.close() def test_five_a(self): handle = StringIO(phylip_text5a) list5 = list(PhylipIterator(handle)) handle.close() self.assertEqual(len(list5), 1) def test_concatenation(self): handle = StringIO(phylip_text4 + "\n" + phylip_text4) self.assertEqual(len(list(PhylipIterator(handle))), 2) handle = StringIO(phylip_text3 + "\n" + phylip_text4 + "\n\n\n" + phylip_text) self.assertEqual(len(list(PhylipIterator(handle))), 3) def test_write_read(self): handle = StringIO(phylip_text5a) list5 = list(PhylipIterator(handle)) handle.close() handle = StringIO() PhylipWriter(handle).write_file(list5) handle.seek(0) list6 = list(PhylipIterator(handle)) self.assertEqual(len(list5), len(list6)) for a1, a2 in zip(list5, list6): self.assertEqual(len(a1), len(a2)) for r1, r2 in zip(a1, a2): self.assertEqual(r1.id, r2.id) self.assertEqual(str(r1.seq), str(r2.seq)) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)