test_SeqIO
Testing reading clustal format file Clustalw/cw02.aln
 ID = 'gi|4959044|gb|AAD34209.1|AF069', Name='<unknown name>',
 Seq='MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSE...GNRESVV', length=601
 ID = 'gi|671626|emb|CAA85685.1|', Name='<unknown 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='<unknown name>',
 Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
 ID = 'gi|6273284|gb|AF191658.1|AF191', Name='<unknown name>',
 Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
 ID = 'gi|6273287|gb|AF191661.1|AF191', Name='<unknown name>',
 Seq='TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCG...TACCAGA', length=156
 ...
 ID = 'gi|6273291|gb|AF191665.1|AF191', Name='<unknown 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 fasta format file Registry/seqs.fasta
 ID and Name='gi|1348916|gb|G26684|G26684',
 Seq='GATCCCTACCCTTNCCGTTGGTCTCTNTCGCTGACTCGAG...TTATTTC', length=285
 ID and Name='gi|129628|sp|P07175|PARA_AGRTU',
 Seq='MPVVVVASSKGGAGKSTTAVVLGTELAHKGVPVTMLDCDP...KLTEALR', length=222
 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 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 = 'P01892', 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 swiss format file SwissProt/sp016
 ID = 'P01100', Name='FOS_HUMAN',
 Seq='MMFSGFNADYEASSSRCSSASPAGDSLSYYHSPADSFSSM...SPTLLAL', length=380
 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 Registry/EDD_RAT.dat
 ID = 'Q62671', Name='EDD_RAT',
 Seq='ARRERMTAREEASLRTLEGRRRATLLSARQGMMSARGDFL...TKNFGFV', length=920
 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/protein_refseq2.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 = 'X56734.1', 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 = 'DD231055.1', 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 embl format file EMBL/SC10H5.embl
 ID = 'AL031232', Name='SC10H5',
 Seq='GATCAGTAGACCCAGCGACAGCAGGGCGGGGCCCAGCAGG...CGAGCAT', length=4870
 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/U87107.embl
 ID = 'U87107.1', Name='U87107',
 Seq='CAATTACTGCAATGCCCTCGTAATTAAGTGAATTTACAAT...CATCACC', length=8840
 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