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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 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/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
- [2jmj7l5rSw0yVb/vlWAYkK/YBwk] len 0, 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/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
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