test_BioSQL_SeqIO
Connecting to database
Removing existing sub-database 'biosql-seqio-test' (if exists)
(Re)creating empty sub-database 'biosql-seqio-test'
Testing loading from fasta format file Fasta/lupine.nu
 - GAAAATTCATTTTCTTTGG...TTT [1iE+opvwGOlR9BBosrgiLMXvdeU] len 655, gi|5049839|gb|AI730987.1|AI730987
 - Retrieving by name/display_id 'gi|5049839|gb|AI730987.1|AI730987', OK
Testing loading from fasta format file Fasta/elderberry.nu
 - ATGAAGTTAAGCACTCTTC...TTT [MOHmvqd+xjjhcd2egRP0bJwhk7k] len 2050, gi|4218935|gb|AF074388.1|AF074388
 - Retrieving by name/display_id 'gi|4218935|gb|AF074388.1|AF074388', OK
Testing loading from fasta format file Fasta/phlox.nu
 - TCGAAACCTGCCTAGCAGA...ACC [QxhYcKAIQnOWFoceezpKYYsnyWw] len 623, gi|5052071|gb|AF067555.1|AF067555
 - Retrieving by name/display_id 'gi|5052071|gb|AF067555.1|AF067555', OK
Testing loading from fasta format file Fasta/centaurea.nu
 - CCTGTCACTTAACTTTTTG...GAG [JwtqysZwR77iHUOvgW4T5LiKXZQ] len 1002, gi|4104054|gb|AH007193.1|SEG_CVIGS
 - Retrieving by name/display_id 'gi|4104054|gb|AH007193.1|SEG_CVIGS', OK
Testing loading from fasta format file Fasta/wisteria.nu
 - GCTCCATTTTTTACACATT...TGA [GG28GDPpXT7jd8J/8vfqLGiymPs] len 2551, gi|5817701|gb|AF142731.1|AF142731
 - Retrieving by name/display_id 'gi|5817701|gb|AF142731.1|AF142731', OK
Testing loading from fasta format file Fasta/sweetpea.nu
 - CAGGCTGCGCGGTTTCTAT...GTT [CvyM53A3A6DbluFI9u8lR5r6VB4] len 309, gi|3176602|gb|U78617.1|LOU78617
 - Retrieving by name/display_id 'gi|3176602|gb|U78617.1|LOU78617', OK
Testing loading from fasta format file Fasta/lavender.nu
 - GGCTCTTAAGTCATGTCTA...GTG [DmX8RD5xSC9EQ4JWVTGXfZGGBOs] len 550, gi|5690369|gb|AF158246.1|AF158246
 - Retrieving by name/display_id 'gi|5690369|gb|AF158246.1|AF158246', OK
Testing loading from fasta format file Fasta/aster.pro
 - GGHVNPAVTFGAFVGGNIT...ANI [WpoEuoNHihSLr/+PA+QufKYpKeg] len 107, gi|3298468|dbj|BAA31520.1|
 - Retrieving by name/display_id 'gi|3298468|dbj|BAA31520.1|', OK
Testing loading from fasta format file Fasta/loveliesbleeding.pro
 - XAGLPVIMCLKSNNHQKYL...QNN [y11wq8yF5uIqrbGtom8ewOB3N4k] len 304, gi|2781234|pdb|1JLY|B
 - Retrieving by name/display_id 'gi|2781234|pdb|1JLY|B', OK
Testing loading from fasta format file Fasta/rose.pro
 - MENSDSNDKGSDQSAAQRR...SVV [4TM+FYSrarRxWPV/dp0LkxEOnSY] len 600, gi|4959044|gb|AAD34209.1|AF069992_1
 - Retrieving by name/display_id 'gi|4959044|gb|AAD34209.1|AF069992_1', OK
Testing loading from fasta format file Fasta/rosemary.pro
 - MSPQTETKASVGFKAGVKE...AMD [gh9uVVLTTrZWSyiacV8RlD4+fBs] len 473, gi|671626|emb|CAA85685.1|
 - Retrieving by name/display_id 'gi|671626|emb|CAA85685.1|', OK
Testing loading from fasta format file Fasta/f001
 - MENLNMDLLYMAAAVMMGL...AVA [H6DUOjvvYInz6g6Z5i7USAMSbc0] len 79, gi|3318709|pdb|1A91|
 - Retrieving by name/display_id 'gi|3318709|pdb|1A91|', OK
Testing loading from fasta format file Fasta/f002
 - CGGACCAGACGGACACAGG...TNA [fgjbiE7hX1FSJU8sZoEq1EiX/k4] len 633, gi|1348912|gb|G26680|G26680
 - Retrieving by name/display_id 'gi|1348912|gb|G26680|G26680', OK
 - CGGAGCCAGCGAGCATATG...AAA [xDJC5Xy7jZ7nRJUdMvoHju48f7E] len 413, gi|1348917|gb|G26685|G26685
 - Retrieving by name/display_id 'gi|1348917|gb|G26685|G26685', OK
 - GATCAAATCTGCACTGTGT...TTT [7QP4Mkyp9wsT38pTuHKVR9x/s7E] len 471, gi|1592936|gb|G29385|G29385
 - Retrieving by name/display_id 'gi|1592936|gb|G29385|G29385', OK
Testing loading from fasta format file Fasta/fa01
 - CPDSINAALICRGEKMSIA...AIA [v3m0kBWRdq8KKKkFDeKa7U3yJV8] len 378, AK1H_ECOLI/1-378
 - Retrieving by name/display_id 'AK1H_ECOLI/1-378', OK
 - -----------------VE...QAN [5tDyl5+50BjsrO8EFmmhzDpyitQ] len 382, AKH_HAEIN/1-382
 - Retrieving by name/display_id 'AKH_HAEIN/1-382', OK
Testing loading from fasta format file GFF/NC_001802.fna
 - GGTCTCTCTGGTTAGACCA...TTC [RHCiFz9D2i0Vz8A01p+n/wk038I] len 9181, gi|9629357|ref|NC_001802.1|
 - Retrieving by name/display_id 'gi|9629357|ref|NC_001802.1|', OK
Testing loading from fasta format file GFF/multi.fna
 - ACGTCGCG [+luRMg1D6rVqqqcgBgMsDttqJpA] len 8, test1
 - Retrieving by name/display_id 'test1', OK
 - GGGGCCCC [VjfJ8qmlO0nL2P1U+6Zi8X1TtMs] len 8, test2
 - Retrieving by name/display_id 'test2', OK
 - AAACACAC [CVAZ5QcTnXq6yn+w5Skgc1v/uw0] len 8, test3
 - Retrieving by name/display_id 'test3', OK
Testing loading from fasta format file Registry/seqs.fasta
 - GATCCCTACCCTTNCCGTT...TTC [Ixmhpsy/UMiI0CGBTBDaNETs1/o] len 285, gi|1348916|gb|G26684|G26684
 - Retrieving by name/display_id 'gi|1348916|gb|G26684|G26684', OK
 - MPVVVVASSKGGAGKSTTA...ALR [2/ffXCsl+1nkvSevuqm/p+qEaNw] len 222, gi|129628|sp|P07175|PARA_AGRTU
 - Retrieving by name/display_id 'gi|129628|sp|P07175|PARA_AGRTU', OK
Testing loading from swiss format file SwissProt/sp001
 - MGARGAPSRRRQAGRRLRY...DFE [c3fT2ic/6G/6gBCedsC+6smMsfk] len 348, Q13454
 - Retrieving by name/display_id 'N33_HUMAN', OK
 - Retrieving by accession 'Q14912', Failed
 - Retrieving by accession 'Q14911', Failed
 - Retrieving by accession 'Q13454', OK
Testing loading from swiss format file SwissProt/sp002
 - MADQRQRSLSTSGESLYHV...GFN [PkMCOc0s3lly64iRyfhbezR8dJI] len 198, P54101
 - Retrieving by name/display_id 'CSP_MOUSE', OK
 - Retrieving by accession 'P54101', OK
Testing loading from swiss format file SwissProt/sp003
 - MDDREDLVYQAKLAEQAER...ENQ [mnuAjdnQZbMFojll2PnV3xFklXQ] len 255, P42655
 - Retrieving by name/display_id '143E_HUMAN', OK
 - Retrieving by accession 'P42655', OK
 - Retrieving by accession 'Q63631', Failed
 - Retrieving by accession 'P29360', Failed
Testing loading from swiss format file SwissProt/sp004
 - TVKWIEAVALSDILEGDVL...DLS [ZRv7OfNYSCSMkMJJmNt8LPaNxYI] len 103, P23082
 - Retrieving by name/display_id 'NDOA_PSEPU', OK
 - Retrieving by accession 'O07829', Failed
 - Retrieving by accession 'P23082', OK
 - Retrieving by accession 'Q52123', Failed
Testing loading from swiss format file SwissProt/sp005
 - MNLLLTLLTNTTLALLLVF...WAE [wjowOf4EEDVZRzZOQsvSdvA9ZZk] len 115, P24973
 - Retrieving by name/display_id 'NU3M_BALPH', OK
 - Retrieving by accession 'P24973', OK
Testing loading from swiss format file SwissProt/sp006
 - MTPHTHVRGPGDILQLTMA...KPR [dZ/Wkfhnezoiqnd1MkL1+get0zI] len 339, P39896
 - Retrieving by name/display_id 'TCMO_STRGA', OK
 - Retrieving by accession 'P39896', OK
Testing loading from swiss format file SwissProt/sp007
 - MANAGLQLLGFILAFLGWI...DYV [38MxEaRUYqwdpkJgOUMtw0/gJsY] len 211, O95832
 - Retrieving by name/display_id 'CLD1_HUMAN', OK
 - Retrieving by accession 'O95832', OK
Testing loading from swiss format file SwissProt/sp008
 - MAVMAPRTLVLLLSGALAL...CKV [oTL0BWZeACoxMc++WgT0XDz+sNg] len 365, P01892
 - Retrieving by name/display_id '1A02_HUMAN', OK
 - Retrieving by accession 'Q29837', Failed
 - Retrieving by accession 'Q29680', Failed
 - Retrieving by accession 'P30445', Failed
 - Retrieving by accession 'P30444', Failed
 - Retrieving by accession 'P30446', Failed
 - Retrieving by accession 'Q29899', Failed
 - Retrieving by accession 'P30514', Failed
 - Retrieving by accession 'Q95380', Failed
 - Retrieving by accession 'P01892', OK
 - Retrieving by accession 'Q95352', Failed
 - Retrieving by accession 'P06338', Failed
Testing loading from swiss format file SwissProt/sp009
 - MAPAMEEIRQAQRAEGPAA...GAE [5Y08l+HJRDIlhLKzFEfkcKd1dkM] len 394, O23729
 - Retrieving by name/display_id 'CHS3_BROFI', OK
 - Retrieving by accession 'O23729', OK
Testing loading from swiss format file SwissProt/sp010
 - MDKLDANVSSEEGFGSVEK...SDT [5+1AMJ2Bq46D7PZcb+0pVHgBY/U] len 388, Q13639
 - Retrieving by name/display_id '5H4_HUMAN', OK
 - Retrieving by accession 'Q9UBT4', Failed
 - Retrieving by accession 'Q13639', OK
 - Retrieving by accession 'Q9UE22', Failed
 - Retrieving by accession 'Q9UE23', Failed
 - Retrieving by accession 'Q9NY73', Failed
 - Retrieving by accession 'Q9UQR6', Failed
 - Retrieving by accession 'Q9UBM6', Failed
Testing loading from swiss format file SwissProt/sp011
 - MGRRVPALRQLLVLAVLLL...LTH [u5J0gYBDy6pkr5W50INxN5oTpfc] len 700, P16235
 - Retrieving by name/display_id 'LSHR_RAT', OK
 - Retrieving by accession 'Q63808', Failed
 - Retrieving by accession 'Q63807', Failed
 - Retrieving by accession 'Q63809', Failed
 - Retrieving by accession 'P70646', Failed
 - Retrieving by accession 'P16235', OK
Testing loading from swiss format file SwissProt/sp012
 - MQIFVKTLTGKTITLEVES...GGN [IKk9x9IFxI3MfuQZK5Yj6GqrMoI] len 153, Q9Y736
 - Retrieving by name/display_id 'Q9Y736', OK
 - Retrieving by accession 'Q9Y736', OK
Testing loading from swiss format file SwissProt/sp013
 - MGSKMASASRVVQVVKPHT...GPE [T8BbsFK2PbHRp+GbdYcTN9Bntg8] len 102, P82909
 - Retrieving by name/display_id 'P82909', OK
 - Retrieving by accession 'P82909', OK
Testing loading from swiss format file SwissProt/sp014
 - TQSNPNEQNVELNRTSLYW...FFN [2HGMj0JzBD6fB77zuXb7d40NQ8E] len 37, P12166
 - Retrieving by name/display_id 'PSBL_ORYSA', OK
 - Retrieving by accession 'P12166', OK
 - Retrieving by accession 'P12167', Failed
 - Retrieving by accession 'Q34007', Failed
Testing loading from swiss format file SwissProt/sp015
 - MSFQAPRRLLELAGQSLLR...TPC [rlLDtS0YQpxxe4PpiRjzJqFBWws] len 457, IPI00383150
 - Retrieving by name/display_id 'IPI00383150.2', OK
 - Retrieving by accession 'IPI00383150', OK
Testing loading from swiss format file SwissProt/sp016
 - MMFSGFNADYEASSSRCSS...LAL [R09jzTKeAyzIQYTQAsps2UWFyFE] len 380, P01100
 - Retrieving by name/display_id 'FOS_HUMAN', OK
 - Retrieving by accession 'P18849', Failed
 - Retrieving by accession 'P01100', OK
Testing loading from swiss format file Registry/EDD_RAT.dat
 - ARRERMTAREEASLRTLEG...GFV [lZx7bXx+In1Zm7KYv4OlWRUhy7g] len 920, Q62671
 - Retrieving by name/display_id 'EDD_RAT', OK
 - Retrieving by accession 'Q62671', OK
Testing loading from genbank format file GenBank/noref.gb
 - GGCAAGATGGCGCCGGTGG...AAA [OYTVZwtXljz/URn1+Yiv/qiMyy8] len 1622, NM_006141.1
 - Retrieving by name/display_id 'NM_006141', OK
 - Retrieving by version 'NM_006141.1', OK
 - Retrieving by accession 'NM_006141', OK
 - Retrieving by GI '5453633', OK
Testing loading from genbank format file GenBank/cor6_6.gb
 - AACAAAACACACATCAAAA...AAA [SabZaA4V2eLE9/2Fm5FnyYy07J4] len 513, X55053.1
 - Retrieving by name/display_id 'ATCOR66M', OK
 - Retrieving by version 'X55053.1', OK
 - Retrieving by accession 'X55053', OK
 - Retrieving by GI '16229', OK
 - ATTTGGCCTATAAATATAA...ATA [l7gjJFE6W/S1jJn5+1ASrUKW/FA] len 880, X62281.1
 - Retrieving by name/display_id 'ATKIN2', OK
 - Retrieving by version 'X62281.1', OK
 - Retrieving by accession 'X62281', OK
 - Retrieving by GI '16353', OK
 - AAAAAAACACAACAAAACT...TTC [TtWsXo45S3ZclIBy4X/WJc39+CY] len 441, M81224.1
 - Retrieving by name/display_id 'BNAKINI', OK
 - Retrieving by version 'M81224.1', OK
 - Retrieving by accession 'M81224', OK
 - Retrieving by GI '167145', OK
 - GGACAAGGCCAAGGATGCT...GGC [/wQvmrl87QWcm9llO4/efg23Vgg] len 206, AJ237582.1
 - Retrieving by name/display_id 'ARU237582', OK
 - Retrieving by version 'AJ237582.1', OK
 - Retrieving by accession 'AJ237582', OK
 - Retrieving by GI '4538892', OK
 - AACAAAACTCAATAAATAA...TTT [BUg6YxXSKWEcFFH0L08JzaLGhQs] len 282, L31939.1
 - Retrieving by name/display_id 'BRRBIF72', OK
 - Retrieving by version 'L31939.1', OK
 - Retrieving by accession 'L31939', OK
 - Retrieving by GI '1209261', OK
 - ATGGCAGACAACAAGCAGA...TAG [uVEYeAQSV5EDQOnFoeMmVea+Oow] len 497, AF297471.1
 - Retrieving by name/display_id 'AF297471', OK
 - Retrieving by version 'AF297471.1', OK
 - Retrieving by accession 'AF297471', OK
 - Retrieving by GI '10121868', OK
Testing loading from genbank format file GenBank/iro.gb
 - CACAGGCCCAGAGCCACTC...AAA [7P6ThjKwpVuH+5V3npBraPFagRM] len 1326, AL109817.1
 - Retrieving by name/display_id 'IRO125195', OK
 - Retrieving by version 'AL109817.1', OK
 - Retrieving by accession 'AL109817', OK
 - Retrieving by GI '5731880', OK
Testing loading from genbank format file GenBank/pri1.gb
 - GATCATGCATGCACTCCAG...GCA [lkGSk4qQ7aOFBsIqAI2EOd4Tk0Y] len 741, U05344.1
 - Retrieving by name/display_id 'HUGLUT1', OK
 - Retrieving by version 'U05344.1', OK
 - Retrieving by accession 'U05344', OK
 - Retrieving by GI '452475', OK
Testing loading from genbank format file GenBank/arab1.gb
 - AAGCTTTGCTACGATCTAC...CTT [BGuIPJXJ8FT0DHoOjAbXgAjjVFw] len 86436, AC007323.5
 - Retrieving by name/display_id 'AC007323', OK
 - Retrieving by version 'AC007323.5', OK
 - Retrieving by accession 'AC007323', OK
 - Retrieving by GI '6587720', OK
Testing loading from genbank format file GenBank/protein_refseq2.gb
 - MNNRWILHAAFLLCFSTTA...FQN [+/OSLiyGWcFWiLWgW/xDKe+6Ml8] len 182, NP_034640.1
 - Retrieving by name/display_id 'NP_034640', OK
 - Retrieving by version 'NP_034640.1', OK
 - Retrieving by accession 'NP_034640', OK
 - Retrieving by GI '6754304', OK
Testing loading from genbank format file GenBank/extra_keywords.gb
 - TCCAGGGGATTCACGCGCA...TTG [Gp6GqZ3Q9foPG0HvyXguIGSJN8U] len 154329, AL138972.1
 - Retrieving by name/display_id 'DMBR25B3', OK
 - Retrieving by version 'AL138972.1', OK
 - Retrieving by accession 'AL138972', OK
 - Retrieving by GI '6946668', OK
Testing loading from genbank format file GenBank/one_of.gb
 - GAATTCAGATAGAATGTAG...GGC [CRSBthp5vOPFSGq9eJRxKFnMg8k] len 2509, U18266.1
 - Retrieving by name/display_id 'HSTMPO1', OK
 - Retrieving by version 'U18266.1', OK
 - Retrieving by accession 'U18266', OK
 - Retrieving by GI '885676', OK
Testing loading from genbank format file GenBank/NT_019265.gb
 - UnknownSeq(1250660, alphabet = IUPACAmbiguousDNA(), character = 'N'), NT_019265.6
 - Retrieving by name/display_id 'NT_019265', OK
 - Retrieving by version 'NT_019265.6', OK
 - Retrieving by accession 'NT_019265', OK
 - Retrieving by GI '16156830', OK
Testing loading from genbank format file GenBank/origin_line.gb
 - TTAATTAACTGTCTTCGAT...CGC [z67vvxaMmqQ1AtM2COP5QGIOQNY] len 180, NC_002678.1
 - Retrieving by name/display_id 'NC_002678', OK
 - Retrieving by version 'NC_002678.1', OK
 - Retrieving by accession 'NC_002678', OK
 - Retrieving by GI '13470324', OK
Testing loading from genbank format file GenBank/blank_seq.gb
 - MEECWVTEIANGSKDGLDS...SDC [tOzrkRHM0nOinnvHIdURS9h1HVc] len 360, NP_001832.1
 - Retrieving by name/display_id 'NP_001832', OK
 - Retrieving by version 'NP_001832.1', OK
 - Retrieving by accession 'NP_001832', OK
 - Retrieving by GI '4502929', OK
Testing loading from genbank format file GenBank/dbsource_wrap.gb
 - VKDGYIVDDRNCTYFCGRN...RCN [9+rXFOVCXjw3X42lNvbjj08gXhI] len 64, P01485
 - Retrieving by name/display_id 'SCX3_BUTOC', OK
 - Retrieving by accession 'P01485', OK
 - Retrieving by GI '134354', OK
Testing loading from genbank format file GenBank/NC_005816.gb
 - TGTAACGAACGGTGCAATA...CTG [BJyiVBblVozP/evddBBrOxC9Rwo] len 9609, NC_005816.1
 - Retrieving by name/display_id 'NC_005816', OK
 - Retrieving by version 'NC_005816.1', OK
 - Retrieving by accession 'NC_005816', OK
 - Retrieving by GI '45478711', OK
Testing loading from genbank format file GenBank/gbvrl1_start.seq
 - ATGTCTGGCAACCAGTATA...TAA [iOtYxMtQxgFhtAHI3B7A6aI5ypY] len 2007, AB000048.1
 - Retrieving by name/display_id 'AB000048', OK
 - Retrieving by version 'AB000048.1', OK
 - Retrieving by accession 'AB000048', OK
 - Retrieving by GI '1769753', OK
 - ATGTCTGGCAACCAGTATA...TAA [vVpAeQbUf2E0m6rwVEiMhMEdjbU] len 2007, AB000049.1
 - Retrieving by name/display_id 'AB000049', OK
 - Retrieving by version 'AB000049.1', OK
 - Retrieving by accession 'AB000049', OK
 - Retrieving by GI '1769755', OK
 - ATGAGTGATGGAGCAGTTC...TAA [o1g2BqevdWX2pm+X8Hjhkp+J1P4] len 1755, AB000050.1
 - Retrieving by name/display_id 'AB000050', OK
 - Retrieving by version 'AB000050.1', OK
 - Retrieving by accession 'AB000050', OK
 - Retrieving by GI '1769757', OK
Testing loading from genbank format file GFF/NC_001422.gbk
 - GAGTTTTATCGCTTCCATG...GCA [NOAEKZNTbMxBsWQQ7JQrnWMXQLo] len 5386, NC_001422.1
 - Retrieving by name/display_id 'NC_001422', OK
 - Retrieving by version 'NC_001422.1', OK
 - Retrieving by accession 'NC_001422', OK
 - Retrieving by GI '9626372', OK
Testing loading from embl format file EMBL/TRBG361.embl
 - AAACAAACCAAATATGGAT...AAA [jfp/7BKv3jTJAU/4jVMrSftEq20] len 1859, X56734.1
 - Retrieving by name/display_id 'X56734', OK
 - Retrieving by version 'X56734.1', OK
 - Retrieving by accession 'S46826', Failed
 - Retrieving by accession 'X56734', OK
Testing loading from embl format file EMBL/DD231055_edited.embl
 - GCCGAGCTGACCCAGTCTC...AGA [HckQPCOck1ENHObieZ97zzyeVsg] len 315, DD231055.1
 - Retrieving by name/display_id 'DD231055', OK
 - Retrieving by version 'DD231055.1', OK
 - Retrieving by accession 'DD231055', OK
Testing loading from embl format file EMBL/SC10H5.embl
 - GATCAGTAGACCCAGCGAC...CAT [qdRtCppTP7VPQHUzRkXQ4qsMCAE] len 4870, AL031232
 - Retrieving by name/display_id 'SC10H5', OK
 - Retrieving by accession 'AL031232', OK
Testing loading from embl format file EMBL/U87107.embl
 - CAATTACTGCAATGCCCTC...ACC [2pQRlTpkQXDbP6ZajjG6vRd9u/Q] len 8840, U87107.1
 - Retrieving by name/display_id 'U87107', OK
 - Retrieving by version 'U87107.1', OK
 - Retrieving by accession 'U87107', OK
Removing (deleting) 'biosql-seqio-test'
Committing remaining changes
Closing connection