[Biopython-dev] [Bug 2289] Can't parse GenBank files with "ss-cRNA" in the LOCUS line

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2289





------- Comment #5 from Daniel.Nicorici at gmail.com  2007-05-09 10:57 EST -------
Here is the part of the file that generates the error:
=======================================================================
LOCUS       NC_005236               1769 bp ss-cRNA    linear   VRL 20-FEB-2007
DEFINITION  Seoul virus strain 80-39 segment S, complete sequence.
ACCESSION   NC_005236
VERSION     NC_005236.1  GI:38505529
PROJECT     GenomeProject:15027
KEYWORDS    .
SOURCE      Seoul virus
  ORGANISM  Seoul virus
            Viruses; ssRNA negative-strand viruses; Bunyaviridae; Hantavirus.
REFERENCE   1  (bases 1 to 1769)
  AUTHORS   Song,J.-W., Moon,J.Y., Baek,L.J. and Song,K.-J.
  TITLE     Genetic analysis of the full length of S segment of Seoul virus
            prototype, 80-39 strain
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1769)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (12-AUG-2004) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 1769)
  AUTHORS   Song,J.-W., Moon,J.Y., Baek,L.J. and Song,K.-J.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-APR-2003) Department of Microbiology, College of
            Medicine, Korea University, 5-ka, Anam-dong, Sungbuk-ku, Seoul
            136-705, Korea
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AY273791.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..1769
                     /organism="Seoul virus"
                     /mol_type="viral cRNA"
                     /strain="80-39"
                     /isolation_source="Rattus norvegicus"
                     /db_xref="taxon:11608"
                     /segment="segment S"
                     /country="South Korea"
     gene            43..1332
                     /locus_tag="SEOVsSgp1"
                     /db_xref="GeneID:2943086"
     CDS             43..1332
                     /locus_tag="SEOVsSgp1"
                     /codon_start=1
                     /product="nucleocapsid protein"
                     /protein_id="NP_942556.1"
                     /db_xref="GI:38505530"
                     /db_xref="GeneID:2943086"
                     /translation="MATMEEIQREISAHEGQLVIARQKVKDAEKQYEKDPDDLNKRAL
                     HDRESVAASIQSKIDELKRQLADRIAAGKNIGQDRDPTGVEPGDHLKERSALSYGNTL
                     DLNSLDIDEPTGQTADWLTIIVYLTSFVVPIILKALYMLTTRGRQTSKDNKGMRIRFK
                     DDSSYEDVNGIRKPKHLYVSMPNAQSSMKAEEITPGRFRTAVCGLYPAQIKARNMVSP
                     VMSVVGFLALAKDWTSRIEEWLGAPCKFMAESPIAGSLSGNPVNRDYIRQRQGALAGM
                     EPKEFQALRQHSKDAGCTLVEHIESPSSIWVFAGAPDRCPPTCLFVGGMAELGAFFSI
                     LQDMRNTIMASKTVGTADEKLRKKSSFYQSYLRRTQSMGIQLDQRIIVMFMVAWGKEA
                     VDNFHLGDDMDPELRSLAQILIDQKVKEISNQEPMKL"
ORIGIN      
        1 tagtagtaga ctccctaaag agctactcca ctaacaagag aaatggcaac tatggaggaa
       61 atccagagag aaatcagtgc tcacgagggg cagcttgtga tagcacgcca gaaggtcaag
      121 gatgcagaaa agcagtatga gaaggatcct gatgacttaa acaagagggc actgcatgat
      181 cgggagagtg tcgcagcttc aatacaatca aaaattgatg aactgaagcg ccaacttgcc
      241 gacaggattg cagcagggaa gaacatcggg caagaccggg atcctacagg ggtagagccg
      301 ggtgatcatc tcaaggaaag atcagcacta agctacggga atacactgga cctgaatagt
      361 cttgacattg atgaacctac aggacaaaca gctgattggc tgactataat tgtctatcta
      421 acatcattcg tggtcccgat catcttgaag gcactgtaca tgttaacaac aagaggtagg
      481 cagacttcaa aggacaacaa ggggatgagg atcagattca aggatgacag ctcatatgag
      541 gatgtcaatg ggatcagaaa gcctaaacat ctgtatgtgt caatgccaaa cgcccaatcc
      601 agtatgaagg ctgaagagat aacaccagga agattccgca ctgcagtatg tgggctatat
      661 cctgcacaga taaaggcaag gaatatggta agccctgtca tgagtgtagt tgggtttttg
      721 gcactagcaa aagactggac atctagaatt gaagaatggc ttggcgcacc ctgcaagttc
      781 atggcagagt ctcctattgc tgggagttta tctgggaatc ctgtgaatcg tgactatatc
      841 agacaaagac aaggtgcact tgcagggatg gagccaaagg aatttcaagc cctcaggcaa
      901 cattcaaagg atgctggatg tacactagtt gaacatattg agtcaccatc gtcaatatgg
      961 gtgtttgctg gggcccctga taggtgtcca ccaacatgct tgtttgttgg agggatggct
     1021 gagttaggtg ccttcttttc tatacttcag gatatgagga acacaatcat ggcttcaaaa
     1081 actgtgggca cagctgatga aaagcttcga aagaaatcat cattctatca atcatacctc
     1141 agacgcacac aatcaatggg aatacaactg gaccagagga taattgttat gtttatggtt
     1201 gcctggggaa aggaggcagt ggacaacttc catctcggtg atgacatgga tccagagctt
     1261 cgtagcctgg ctcagatctt gattgaccag aaagtgaagg aaatctcgaa ccaggagcct
     1321 atgaaattat aagcacataa atatgtaatc aatactaact ataggttaag aaatactaat
     1381 cattagttaa taagaataca gatttattga ataatcatat taaataatta ggtaagttaa
     1441 atattattta gttaagttag ctaattgatt tatatgatta tcacaattga atgtaatcat
     1501 aagcacaatc actgccatgt ataatcacgg gtatacgggt ggttttcata tggggaacag
     1561 ggtgggctta gggccaggtc accttaagtg accttttttt gtatatatgg atgtagattt
     1621 caattgatcg aatactaatc ctactgtcct cttttctttt cctttctcct tctttactaa
     1681 caacaacaaa ctacctcaca accttctacc tcaatatata ctacctcatt aagttgtttc
     1741 cttttgtctt tttagggagt ctactacta
// 
========================================================================


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