[Bioperl-guts-l] [Bug 2018] Bio::ClusterIO::dbsnp breaks with new XML output

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Mar 9 13:48:14 EST 2007


http://bugzilla.open-bio.org/show_bug.cgi?id=2018





------- Comment #12 from ahawkins at watson.wustl.edu  2007-03-09 13:48 EST -------
Actually, the header of my file does specify a schema location:
<ExchangeSet xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/SNP/docsum
ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_2005.xsd" specVersion="2.0"
dbSnpBuild="126" generated="2006-08-17 02:47">

But it seems that the code in next_cluster is just stepping past the header
info anyway. It appears to be completely ignoring it, as far as I can tell. 

What is the best course of action for this? Should I be getting files from
eutils instead of the ftp site? Do those files always contain the same data
(aside from the conversion you mention)? Can I get the most recent version or
is there a lag? Or would it be better if the parser worked on my version?

-Amy 


(In reply to comment #11)
> Here's the difference:
> 
> Your file (ftp): 
> 
> <ExchangeSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xmlns="http://www.ncbi.nlm.nih.gov/SNP/docsum"    specVersion="2.0"
> dbSnpBuild="126" generated="2006-08-17 02:47">
> 
> My file (from NCBI eutils efetch):
> 
> <?xml version="1.0"?>
> <ExchangeSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xmlns="http://www.ncbi.nlm.nih.gov/SNP/docsum"
> xsi:schemaLocation="http://www.ncbi.nlm.nih.gov/SNP/docsum
> http://www.ncbi.nlm.nih.gov/SNP/docsum/docsum_eutil_ver1.0a.xsd">
> 
> Note the schema location is specified in the latter.  There appears to be a
> conversion of attributes to simple elements in eutils which is causing
> problems. I believe this is the format that the original parser was based on. 
> This will not be an easy fix since the parser expects data being in simple
> tagged elements and not attributes; everything is currently mapped based on
> that expectation.  What a PITA.  
> 


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