[Bioperl-l] Warning message terminates Stream_by_query?

JAMES IBEN jiben at jhu.edu
Wed Jun 2 16:50:57 EDT 2004

Hello list,

  I have written a program (my first) which takes a Genbank 
query and retrieves sequences to pull out an intergenic region 
that I would like to work with.  However, when running the 
program I always at some point run into the following warning 

-------------------- WARNING ---------------------
MSG: Unbalanced quote in:
/product="putative cystathionine beta-lyase"
IVIHSATKFLSGHSDLINo further qualifiers will be added for this 

  With different querys, the message refers to some other 
Genbank sequence (i.e. not always this particular entry).  The 
problem is that once I have run into this message, the 
seqence stream terminates, ending the program.  
  I have checked these entries and see nothing apparantly 
wrong with them (everything is bounded by quotes).  Can 
anyone tell me what this error arises from and perhaps what I 
can do to avoid it (or at least to skip any problematic 
sequences without interrupting the stream)?
  The querys I have been sumitting should only pull about 250 
sequences if they were not interrupted.  Is there some sort of 
stream size limitation that I am hitting?  If there is a problem 
with this approach is there a better solution for my particular 
task than using Stream_by_query?

Thanks for your help,

More information about the Bioperl-l mailing list