[Biopython-dev] [Bug 3026] New: Bio.SeqIO.InsdcIO._split_multi_line(): Your description cannot be broken into nice lines!

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3026

           Summary: Bio.SeqIO.InsdcIO._split_multi_line(): Your description
                    cannot be broken into nice lines!
           Product: Biopython
           Version: 1.53
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mmokrejs at ribosome.natur.cuni.cz


Traceback (most recent call last):
  File "/home/mmokrejs/bin/filter-accessions.py", line 22, in <module>
    SeqIO.write(sequences, output_handle, "genbank")
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 363, in
write
    count = writer_class(handle).write_file(sequences)
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/Interfaces.py", line 271, in
write_file
    count = self.write_records(records)
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/Interfaces.py", line 256, in
write_records
    self.write_record(record)
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/InsdcIO.py", line 691, in
write_record
    self._write_comment(record)
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/InsdcIO.py", line 579, in
_write_comment
    self._write_multi_line("", line)
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/InsdcIO.py", line 335, in
_write_multi_line
    lines = self._split_multi_line(text, max_len)
  File "/usr/lib/python2.6/site-packages/Bio/SeqIO/InsdcIO.py", line 279, in
_split_multi_line
    "Your description cannot be broken into nice lines!"
AssertionError: Your description cannot be broken into nice lines!


Please fix the message so it prints out the accession/version number. ;-)


LOCUS       BF378302                 501 bp    mRNA    linear   EST 27-NOV-2000
DEFINITION  CM0-UM0001-060300-270-g07 UM0001 Homo sapiens cDNA, mRNA sequence.
ACCESSION   BF378302
VERSION     BF378302.1  GI:11367336
KEYWORDS    EST.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 501)
  AUTHORS   Dias Neto,E., Garcia Correa,R., Verjovski-Almeida,S., Briones,M.R.,
            Nagai,M.A., da Silva,W. Jr., Zago,M.A., Bordin,S., Costa,F.F.,
            Goldman,G.H., Carvalho,A.F., Matsukuma,A., Baia,G.S., Simpson,D.H.,
            Brunstein,A., deOliveira,P.S., Bucher,P., Jongeneel,C.V., O'Hare
            ,M.J., Soares,F., Brentani,R.R., Reis,L.F., de Souza,S.J. and
            Simpson,A.J.
  TITLE     Shotgun sequencing of the human transcriptome with ORF expressed
            sequence tags
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 97 (7), 3491-3496 (2000)
   PUBMED   10737800
COMMENT     Contact: Simpson A.J.G.
            Laboratory of Cancer Genetics
            Ludwig Institute for Cancer Research
            Rua Prof. Antonio Prudente 109, 4 andar, 01509-010, Sao Paulo-SP,
            Brazil
            Tel: +55-11-2704922
            Fax: +55-11-2707001
            Email: asimpson at ludwig.org.br
            This sequence was derived from the FAPESP/LICR Human Cancer Genome
            Project. This entry can be seen in the following URL
           
(http://www.ludwig.org.br/scripts/gethtml2.pl?t1=CM0&t2=CM0-UM0001-060300-270-g07&t3=2000-03-06&t4=1
            )
            Seq primer: puc 18 forward.
FEATURES             Location/Qualifiers
[cut]

I have few more example slike this from some dbEST data, I think all from a
same project, though.


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