test_SeqIO Testing reading clustal format file Clustalw/cw02.aln ID = 'gi|4959044|gb|AAD34209.1|AF069', Name='', Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=601 ID = 'gi|671626|emb|CAA85685.1|', Name='', Seq='---------MSPQTETKASVGFKAGVKEYKLTYYTPEYET...PAMD---', length=601 Testing reading clustal format file Clustalw/cw02.aln as an alignment M- alignment column 0 E- alignment column 1 N- alignment column 2 S- alignment column 3 D- alignment column 4 || ... V- alignment column 600 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading clustal format file Clustalw/opuntia.aln ID = 'gi|6273285|gb|AF191659.1|AF191', Name='', Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 ID = 'gi|6273284|gb|AF191658.1|AF191', Name='', Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 ID = 'gi|6273287|gb|AF191661.1|AF191', Name='', Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 ... ID = 'gi|6273291|gb|AF191665.1|AF191', Name='', Seq='TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156 Testing reading clustal format file Clustalw/opuntia.aln as an alignment TTTTTTT alignment column 0 AAAAAAA alignment column 1 TTTTTTT alignment column 2 AAAAAAA alignment column 3 CCCCCCC alignment column 4 ||||||| ... AAAAAAA alignment column 155 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/lupine.nu ID and Name='gi|5049839|gb|AI730987.1|AI730987', Seq='GAAAATTCATTTTCTTTGGACTTTCTCTGAAATCCGAGTC...GGTTTTT', length=655 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/elderberry.nu ID and Name='gi|4218935|gb|AF074388.1|AF074388', Seq='ATGAAGTTAAGCACTCTTCTCATCTTATCTTTTCCTTTCC...GTCGTTT', length=2050 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/phlox.nu ID and Name='gi|5052071|gb|AF067555.1|AF067555', Seq='TCGAAACCTGCCTAGCAGAACGACCCGCGAACTTGTATTC...CACGACC', length=623 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/centaurea.nu ID and Name='gi|4104054|gb|AH007193.1|SEG_CVIGS', Seq='CCTGTCACTTAACTTTTTGTTCATAAGGTATATATGGGGG...GTTAGAG', length=1002 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/wisteria.nu ID and Name='gi|5817701|gb|AF142731.1|AF142731', Seq='GCTCCATTTTTTACACATTTCTATGAACTAATTGGTTCAT...ATGATGA', length=2551 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/sweetpea.nu ID and Name='gi|3176602|gb|U78617.1|LOU78617', Seq='CAGGCTGCGCGGTTTCTATTTATGAAGAACAAGGTCCGTA...GTTTGTT', length=309 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Nucleic/lavender.nu ID and Name='gi|5690369|gb|AF158246.1|AF158246', Seq='GGCTCTTAAGTCATGTCTAGGCAGGTGTGCACAAGTTTAG...GTAGGTG', length=550 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Amino/aster.pro ID and Name='gi|3298468|dbj|BAA31520.1|', Seq='GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLL...FIVGANI', length=107 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Amino/loveliesbleeding.pro ID and Name='gi|2781234|pdb|1JLY|B', Seq='XAGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKIL...IELGQNN', length=304 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Amino/rose.pro ID and Name='gi|4959044|gb|AAD34209.1|AF069992_1', Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=600 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Amino/rosemary.pro ID and Name='gi|671626|emb|CAA85685.1|', Seq='MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAF...FEFPAMD', length=473 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Fasta/f001 ID and Name='gi|3318709|pdb|1A91|', Seq='MENLNMDLLYMAAAVMMGLAAIGAAIGIGILGGKFLEGAA...YVMFAVA', length=79 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file Fasta/f002 ID and Name='gi|1348912|gb|G26680|G26680', Seq='CGGACCAGACGGACACAGGGAGAAGCTAGTTTCTTTCATG...GGTTTNA', length=633 ID and Name='gi|1348917|gb|G26685|G26685', Seq='CGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATC...NNNGAAA', length=413 ID and Name='gi|1592936|gb|G29385|G29385', Seq='GATCAAATCTGCACTGTGTCTACATATAGGAAAGGTCCTG...NTTTTTT', length=471 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Testing reading fasta format file Fasta/fa01 ID and Name='AK1H_ECOLI/1-378', Seq='CPDSINAALICRGEKMSIAIMAGVLEARGH-N--VTVIDP...INIVAIA', length=378 ID and Name='AKH_HAEIN/1-382', Seq='-----------------VEDAVKATIDCRGEKLSIAMMKA...SALAQAN', length=382 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Testing reading fasta format file GFF/NC_001802.fna ID and Name='gi|9629357|ref|NC_001802.1|', Seq='GGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTC...GTGCTTC', length=9181 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file GFF/NC_001802lc.fna ID and Name='gi|9629357|ref|nc_001802.1|', Seq='ggtctctctggttagaccagatctgagcctgggagctctc...gtgcttc', length=9181 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading fasta format file GFF/multi.fna ID and Name='test1', Seq='ACGTCGCG', length=8 ID and Name='test2', Seq='GGGGCCCC', length=8 ID and Name='test3', Seq='AAACACAC', length=8 Testing reading fasta format file GFF/multi.fna as an alignment AGA alignment column 0 CGA alignment column 1 GGA alignment column 2 TGC alignment column 3 CCA alignment column 4 ||| ... GCC alignment column 7 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading nexus format file Nexus/f1.nex ID and Name='t2 the name', Seq='ACGT', length=4 ID and Name='isn'that [a] strange name?', Seq='ACGT', length=4 ID and Name='one should be punished, for (that)!', Seq='ACGT', length=4 ... ID and Name='t9', Seq='cccc', length=4 Testing reading nexus format file Nexus/f1.nex as an alignment AAAAAAc alignment column 0 CCCCCCc alignment column 1 GGGGGGc alignment column 2 TTTTTTc alignment column 3 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading nexus format file Nexus/f2.nex ID and Name='t1', Seq='A-CG-T-gttgtctc-t------a-gttgtctct-t-t', length=38 ID and Name='t2 the name', Seq='A-CGcT-gt----tc-t----aca-gt----tct-t-t', length=38 ID and Name='isn'that [a] strange name?', Seq='A-CGcT-gttgtct------aaca-gttgtct------', length=38 ... ID and Name='t9', Seq='cccccc-ccccccccNc-cccccc-cccccccccNc-c', length=38 Testing reading nexus format file Nexus/f2.nex as an alignment AAAAAAAAc alignment column 0 -----c?tc alignment column 1 CCCCCCCCc alignment column 2 GGGGGGGGc alignment column 3 -cc--tgtc alignment column 4 ||||||||| ... tt--?ag?c alignment column 37 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading nexus format file Nexus/test_Nexus_input.nex ID and Name='t1', Seq='A-C-G-Tc-gtgtgtgctct-t-t------ac-gtgtgtgctct-t-t', length=48 ID and Name='t2 the name', Seq='A-C-GcTc-gtg-----tct-t-t----acac-gtg-----tct-t-t', length=48 ID and Name='isn'that [a] strange name?', Seq='A-CcGcTc-gtgtgtgct--------acacac-gtgtgtgct------', length=48 ... ID and Name='t9', Seq='cccccccc-cccccccccccNc-ccccccccc-cccccccccccNc-c', length=48 Testing reading nexus format file Nexus/test_Nexus_input.nex as an alignment AAAAAAAAc alignment column 0 -----c?tc alignment column 1 CCCCCCCCc alignment column 2 --c-?a-tc alignment column 3 GGGGGGGGc alignment column 4 ||||||||| ... tt--?ag?c alignment column 47 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp001 ID = 'Q13454', Name='N33_HUMAN', Seq='MGARGAPSRRRQAGRRLRYLPTGSFPFLLLLLLLCIQLGG...YSDLDFE', length=348 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp002 ID = 'P54101', Name='CSP_MOUSE', Seq='MADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYRKLAL...YHTDGFN', length=198 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp003 ID = 'P42655', Name='143E_HUMAN', Seq='MDDREDLVYQAKLAEQAERYDEMVESMKKVAGMDVELTVE...DVEDENQ', length=255 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp004 ID = 'P23082', Name='NDOA_PSEPU', Seq='TVKWIEAVALSDILEGDVLGVTVEGKELALYEVEGEIYAT...RVMIDLS', length=103 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp005 ID = 'P24973', Name='NU3M_BALPH', Seq='MNLLLTLLTNTTLALLLVFIAFWLPQLNVYAEKTSPYECG...EGLEWAE', length=115 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp006 ID = 'P39896', Name='TCMO_STRGA', Seq='MTPHTHVRGPGDILQLTMAFYGSRALISAVELDLFTLLAG...AIGRKPR', length=339 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp007 ID = 'O95832', Name='CLD1_HUMAN', Seq='MANAGLQLLGFILAFLGWIGAIVSTALPQWRIYSYAGDNI...SSGKDYV', length=211 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp008 ID = 'Q95352', Name='1A02_HUMAN', Seq='MAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPG...SLTACKV', length=365 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp009 ID = 'O23729', Name='CHS3_BROFI', Seq='MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDY...VPIAGAE', length=394 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp010 ID = 'Q13639', Name='5H4_HUMAN', Seq='MDKLDANVSSEEGFGSVEKVVLLTFLSTVILMAILGNLLV...AAQPSDT', length=388 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp011 ID = 'P16235', Name='LSHR_RAT', Seq='MGRRVPALRQLLVLAVLLLKPSQLQSRELSGSRCPEPCDC...PPRALTH', length=700 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp012 ID and Name='Q9Y736', Seq='MQIFVKTLTGKTITLEVESSDTIDNVKTKIQDKEGIPPDQ...LRLRGGN', length=153 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp013 ID and Name='P82909', Seq='MGSKMASASRVVQVVKPHTPLIRFPDRRDNPKPNVSEALR...IQRGGPE', length=102 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp014 ID = 'P12166', Name='PSBL_ORYSA', Seq='TQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN', length=37 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading swiss format file SwissProt/sp015 ID = 'IPI00383150', Name='IPI00383150.2', Seq='MSFQAPRRLLELAGQSLLRDQALAISVLDELPRELFPRLF...FIGPTPC', length=457 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/noref.gb ID = 'NM_006141.1', Name='NM_006141', Seq='GGCAAGATGGCGCCGGTGGGGGTGGAGAAGAAGCTGCTGC...AAAAAAA', length=1622 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/cor6_6.gb ID = 'X55053.1', Name='ATCOR66M', Seq='AACAAAACACACATCAAAAACGATTTTACAAGAAAAAAAT...AAAAAAA', length=513 ID = 'X62281.1', Name='ATKIN2', Seq='ATTTGGCCTATAAATATAAACCCTTAAGCCCACATATCTT...AATTATA', length=880 ID = 'M81224.1', Name='BNAKINI', Seq='AAAAAAACACAACAAAACTCAATAAATAAACAAATGGCAG...AAGCTTC', length=441 ... ID = 'AF297471.1', Name='AF297471', Seq='ATGGCAGACAACAAGCAGAGCTTCCAAGCCGGTCAAGCCG...CAAGTAG', length=497 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Testing reading genbank format file GenBank/iro.gb ID = 'AL109817.1', Name='IRO125195', Seq='CACAGGCCCAGAGCCACTCCTGCCTACAGGTTCTGAGGGC...AAAAAAA', length=1326 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/pri1.gb ID = 'U05344.1', Name='HUGLUT1', Seq='GATCATGCATGCACTCCAGCCTGGGACAAGAGCGAAACTC...GTTTGCA', length=741 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/arab1.gb ID = 'AC007323.5', Name='AC007323', Seq='AAGCTTTGCTACGATCTACATTTGGGAATGTGAGTCTCTT...GAAGCTT', length=86436 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/protein_refseq.gb ID = 'NP_034640.1', Name='NP_034640', Seq='MNNRWILHAAFLLCFSTTALSINYKQLQLQERTNIRKCQE...LTRNFQN', length=182 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/extra_keywords.gb ID = 'AL138972.1', Name='DMBR25B3', Seq='TCCAGGGGATTCACGCGCAATATGTTTCCCTCGCTCGTCT...TCGATTG', length=154329 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/one_of.gb ID = 'U18266.1', Name='HSTMPO1', Seq='GAATTCAGATAGAATGTAGACAAGAGGGATGGTGAGGAAA...CAAAGGC', length=2509 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/NT_019265.gb ID = 'NT_019265.6', Name='NT_019265', Seq='', length=0 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Non-empty sequences are required Checking can write/read as 'phylip' format Failed: Non-empty sequences are required Checking can write/read as 'stockholm' format Failed: Non-empty sequences are required Testing reading genbank format file GenBank/origin_line.gb ID = 'NC_002678.1', Name='NC_002678', Seq='TTAATTAACTGTCTTCGATTGCGTTTAATTGACGGTTTTC...TCAGCGC', length=180 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/blank_seq.gb ID = 'NP_001832.1', Name='NP_001832', Seq='MEECWVTEIANGSKDGLDSNPMKDYMILSGPQKTAVAVLC...DLDLSDC', length=360 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/dbsource_wrap.gb ID = 'P01485', Name='SCX3_BUTOC', Seq='VKDGYIVDDRNCTYFCGRNAYCNEECTKLKGESGYCQWAS...KGPGRCN', length=64 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading genbank format file GenBank/gbvrl1_start.seq ID = 'AB000048.1', Name='AB000048', Seq='ATGTCTGGCAACCAGTATACTGAGGAAGTTATGGAGGGAG...GGATTAA', length=2007 ID = 'AB000049.1', Name='AB000049', Seq='ATGTCTGGCAACCAGTATACTGAGGAAGTTATGGAGGGAG...GGATTAA', length=2007 ID = 'AB000050.1', Name='AB000050', Seq='ATGAGTGATGGAGCAGTTCAACCAGACGGTGGTCAACCTG...ATATTAA', length=1755 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Testing reading genbank format file GFF/NC_001422.gbk ID = 'NC_001422.1', Name='NC_001422', Seq='GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCG...ACCTGCA', length=5386 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading embl format file EMBL/TRBG361.embl ID and Name='X56734', Seq='AAACAAACCAAATATGGATTTTATTGTAGCCATATTTGCT...AAAAAAA', length=1859 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading embl format file EMBL/DD231055_edited.embl ID and Name='DD231055', Seq='GCCGAGCTGACCCAGTCTCCATCCTCCCTGTCTGCATCTG...TATGAGA', length=315 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading stockholm format file Stockholm/simple.sth ID and Name='AP001509.1', Seq='UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAU...UUAAUGU', length=104 ID and Name='AE007476.1', Seq='AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-U...GUGAGAU', length=104 Testing reading stockholm format file Stockholm/simple.sth as an alignment UA alignment column 0 UA alignment column 1 AA alignment column 2 AA alignment column 3 UU alignment column 4 || ... UU alignment column 103 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading stockholm format file Stockholm/funny.sth ID = 'O83071/192-246', Name='O83071', Seq='MTCRAQLIAVPRASSLAE--AIACAQKM----RVSRVPVYERS', length=43 ID = 'O83071/259-312', Name='O83071', Seq='MQHVSAPVFVFECTRLAY--VQHKLRAH----SRAVAIVLDEY', length=43 ID = 'O31698/18-71', Name='O31698', Seq='MIEADKVAHVQVGNNLEH--ALLVLTKT----GYTAIPVLDPS', length=43 ... ID = 'O31699/88-139', Name='O31699', Seq='EVMLTDIPRLHINDPIMK--GFGMVINN------GFVCVENDE', length=43 Testing reading stockholm format file Stockholm/funny.sth as an alignment MMMEE alignment column 0 TQIVV alignment column 1 CHEMM alignment column 2 RVALL alignment column 3 ASDTT alignment column 4 ||||| ... SYSEE alignment column 42 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/reference_dna.phy ID and Name='Archaeopt', Seq='CGATGCTTACCGC', length=13 ID and Name='Hesperorni', Seq='CGTTACTCGTTGT', length=13 ID and Name='Baluchithe', Seq='TAATGTTAATTGT', length=13 ... ID and Name='B.subtilis', Seq='GGCAGCCAATCAC', length=13 Testing reading phylip format file Phylip/reference_dna.phy as an alignment CCTTCG alignment column 0 GGAAAG alignment column 1 ATAAAC alignment column 2 TTTTAA alignment column 3 GAGGAG alignment column 4 |||||| ... CTTTTC alignment column 12 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/reference_dna2.phy ID and Name='Archaeopt', Seq='CGATGCTTACCGCCGATGCTTACCGCCGATGCTTACCGC', length=39 ID and Name='Hesperorni', Seq='CGTTACTCGTTGTCGTTACTCGTTGTCGTTACTCGTTGT', length=39 ID and Name='Baluchithe', Seq='TAATGTTAATTGTTAATGTTAATTGTTAATGTTAATTGT', length=39 ... ID and Name='B.subtilis', Seq='GGCAGCCAATCACGGCAGCCAATCACGGCAGCCAATCAC', length=39 Testing reading phylip format file Phylip/reference_dna2.phy as an alignment CCTTCG alignment column 0 GGAAAG alignment column 1 ATAAAC alignment column 2 TTTTAA alignment column 3 GAGGAG alignment column 4 |||||| ... CTTTTC alignment column 38 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/hennigian.phy ID and Name='A', Seq='CACACACAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='B', Seq='CACACAACAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='C', Seq='CACAACAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA', length=40 ... ID and Name='J', Seq='ACAAAAAAAAACAAAAACACAAAAAAAAAAAAAAAAAAAA', length=40 Testing reading phylip format file Phylip/hennigian.phy as an alignment CCCCCAAAAA alignment column 0 AAAAACCCCC alignment column 1 CCCAAAAAAA alignment column 2 AAACCAAAAA alignment column 3 CCAAAAAAAA alignment column 4 |||||||||| ... AAAAAAAAAA alignment column 39 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/horses.phy ID and Name='Mesohippus', Seq='AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='Hypohippus', Seq='AAACCCCCCCAAAAAAAAACAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='Archaeohip', Seq='CAAAAAAAAAAAAAAAACACAAAAAAAAAAAAAAAAAAAA', length=40 ... ID and Name='Pliohippus', Seq='CCCACCCCCCCCCACACCCCAAAAAAAAAAAAAAAAAAAA', length=40 Testing reading phylip format file Phylip/horses.phy as an alignment AACCCCCCCC alignment column 0 AAAACCCCCC alignment column 1 AAAAAAAAAC alignment column 2 ACAAAAAAAA alignment column 3 ACACCCCCCC alignment column 4 |||||||||| ... AAAAAAAAAA alignment column 39 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/random.phy ID and Name='A', Seq='CACACAACCAAACAAACCACAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='B', Seq='AAACCACACACACAAACCCAAAAAAAAAAAAAAAAAAAAA', length=40 ID and Name='C', Seq='ACAAAACCAAACCACCCACAAAAAAAAAAAAAAAAAAAAA', length=40 ... ID and Name='J', Seq='CCAAAAACACCCAACCCAACAAAAAAAAAAAAAAAAAAAA', length=40 Testing reading phylip format file Phylip/random.phy as an alignment CAAAACAAAC alignment column 0 AACAACCACC alignment column 1 CAAAACAAAA alignment column 2 ACAACACACA alignment column 3 CCAAAACCAA alignment column 4 |||||||||| ... AAAAAAAAAA alignment column 39 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/interlaced.phy ID and Name='CYS1_DICDI', Seq='-----MKVILLFVLAVFTVFVSS---------------RG...STSII--', length=384 ID and Name='ALEU_HORVU', Seq='MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRA...SYPVVAA', length=384 ID and Name='CATH_HUMAN', Seq='------MWATLPLLCAGAWLLGV--------PVCGAAELS...SYPIPLV', length=384 Testing reading phylip format file Phylip/interlaced.phy as an alignment -M- alignment column 0 -A- alignment column 1 -H- alignment column 2 -A- alignment column 3 -R- alignment column 4 ||| ... -AV alignment column 383 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing reading phylip format file Phylip/interlaced2.phy ID and Name='IXI_234', Seq='TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID and Name='IXI_235', Seq='TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCC...AGDRSHE', length=131 ID and Name='IXI_236', Seq='TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCC...AGDRSHE', length=131 ID and Name='IXI_237', Seq='TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----C...AGDRSHE', length=131 Testing reading phylip format file Phylip/interlaced2.phy as an alignment TTTT alignment column 0 SSSS alignment column 1 PPPP alignment column 2 AAAA alignment column 3 SSSS alignment column 4 |||| ... EEEE alignment column 130 Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Finished tested reading files Starting testing writing records (Note that some of these are expected to 'fail' and say why) Testing can write/read zero records Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Must have at least one sequence Checking can write/read as 'phylip' format Failed: Must have at least one sequence Checking can write/read as 'stockholm' format Failed: Must have at least one sequence Testing can write/read three peptides of different lengths Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Failed: Sequences must all be the same length Checking can write/read as 'phylip' format Failed: Sequences must all be the same length Checking can write/read as 'stockholm' format Failed: Sequences must all be the same length Testing can write/read three proteins alignment Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing can write/read three DNA sequence alignment Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing can write/read 3 DNA seq alignment with CR/LF in name/descr Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Checking can write/read as 'stockholm' format Testing can write/read alignment with repeated record Checking can write/read as 'fasta' format Checking can write/read as 'clustal' format Checking can write/read as 'phylip' format Failed: Repeated identifier, possibly due to truncation Checking can write/read as 'stockholm' format Failed: Duplicate record identifier: Beta Finished tested writing files