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Old 04-26-2013, 09:25 AM   #1
Mark
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Default 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.

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Mark
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Old 04-26-2013, 12:35 PM   #2
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Which release of BioPerl are you using?
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Old 04-27-2013, 07:02 AM   #3
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version 1.006901
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Old 04-27-2013, 09:02 AM   #4
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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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Old 04-27-2013, 10:00 AM   #5
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Unfortunately, you can't get the hit description via that method, a serious shortcoming.
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Old 04-27-2013, 10:01 AM   #6
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Quote:
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 at 10:16 AM.
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Old 04-27-2013, 12:33 PM   #7
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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.
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Old 04-27-2013, 03:43 PM   #8
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You mean stitle/salltitles? But yeah, 2.2.28+ only.
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Old 04-27-2013, 03:49 PM   #9
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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.
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Old 04-27-2013, 04:22 PM   #10
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Maybe your problem is related to an outdated XML::SAX? (first note). Just an idea..
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