[Bioperl-l] Problems downloading and parsing GenBank records

[Moller, Abraham]

Hi all,

I have been using a script to parse GenBank files to find taxonomic
information corresponding to bacterial genomes. After several tries, my
script has failed with the following error:

...
Bacteria_Actinobacteria_Streptomycetales_Streptomycetaceae_Streptomyces_Streptomyces_sp._4F
Bacteria_Actinobacteria_Streptomycetales_Streptomycetaceae_Streptomyces_Streptomyces_glaucescens
--------------------- WARNING ---------------------
MSG: Unbalanced quote in:
/locus_tag="M271_25565"
/inference="COORDINATES: ab initio prediction:GeneMarkS+"
/note="Derived by automated computational analysis using
gene prediction method: GeneMarkS+."
/codon_start=1
/transl_table=11
/product="membrane protein"
/protein_id="YP_008791527.1"
/db_xref="GeneID:17596261"
/translation="MPSPTSLAPAGPTATPTRTTATARRLMAICGTLLAALLCALSVG
ANSASAHAALTSTDPADGSVVKTAPREVTLNFSEGVLLSGDSVRVLDPKGKRVDTGKT
AHVDGKSSTAAAGLHSGLPDG Error: External viewer error: Empty Response. Bytes
read: 0 Status: TimeoutNo further qualifiers will be added for this feature
---------------------------------------------------`

After this, the script seems to halt for hours at least, if not
indefinitely...
Is this a BioPerl or GenBank issue? Any help would be appreciated.
Thanks,
Jon Moller

-- 
Abraham (Jon) Moller
Microbiology and Chemistry | 2016
Cell, Molecular, and Structural Biology (CMSB) BS/MS | Liang Bioinfo Lab
Microbiology Club President
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