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bioperl / bioperl-live

Core BioPerl 1.x code
http://bioperl.org
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Problems downloading and parsing GenBank records #232

Closed molleraj closed 7 years ago

molleraj commented 7 years ago

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.

cjfields commented 7 years ago

Hi @molleraj this appears to have been addressed via our discussion on the mail list. Closing, but feel free to reopen if you feel this is a bug in Bioperl