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  • rhinoceros
    replied
    Maybe your problem is related to an outdated XML::SAX? (first note). Just an idea..

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  • Mark
    replied
    Yea, I know but I don't do the blast updates for our system and so can't take that route to a fix. Thanks for trying to help though.

    Leave a comment:


  • rhinoceros
    replied
    You mean stitle/salltitles? But yeah, 2.2.28+ only.

    Leave a comment:


  • Mark
    replied
    Subject description. Yes I know you could grab the oridinal ID and the go back to the blastdb and pull out the record and parse it's description from there but that's a bit of a pain so I would rather find out if there is a solution to the parsing of the xml output.

    Leave a comment:


  • rhinoceros
    replied
    Originally posted by Mark View Post
    Unfortunately, you can't get the hit description via that method, a serious shortcoming.
    What do you mean by hit description? There are like 40 fields to choose from..
    Last edited by rhinoceros; 04-27-2013, 10:16 AM.

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  • Mark
    replied
    Unfortunately, you can't get the hit description via that method, a serious shortcoming.

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  • rhinoceros
    replied
    Can't really help you there but have you considered other output formats (e.g. outfmt 6) and simply parsing your files with unix commands?

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  • Mark
    replied
    version 1.006901

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  • kmcarr
    replied
    Which release of BioPerl are you using?

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  • Mark
    started a topic bioperl blast parsing problem

    bioperl blast parsing problem

    We recently upgraded our installation of blast from v2.2.19 to blast+ 2.2.26 and I have found that my bioperl blast xml parsers no longer work properly (typically they return some form of truncated result). Has anyone else encountered this and if this is a known problem have either the NCBI or BioPerl folks provided a solution.

    Thanks

    Mark

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