Changeset 230


Ignore:
Timestamp:
Sep 29, 2009, 8:16:12 PM (11 years ago)
Author:
pvkouteren
Message:

Bugfixes (mostly regarding calls to the logger)

File:
1 edited

Legend:

Unmodified
Added
Removed
  • parsers/msigdb2.py

    r225 r230  
    2929        p = make_parser()
    3030        msig_handler = MSigDBXMLHandler()
     31        setattr(msig_handler, 'logger', self.logger)
    3132        p.setContentHandler(msig_handler)
    3233        p.parse(self.filename)
     
    7677                    ("Number of outputs from database (%i) " +
    7778                    "does not match the number requested (%i).")
    78                     % (genes_out, genes_in)
     79                    % (nr_genes_out, nr_genes_in)
    7980            )
    8081            missing = gu[:, ('gene', )].omit(genes_uniq[:,('value', )])
     
    9697        self.set_gene = self.set_gene.join(genes_uniq, 'gene', 'value')
    9798        nr_genes_out = len(self.set_gene)
    98         if(not genes_in == genes_out):
    99             self.logging.warning( \
     99        if(not nr_genes_in == nr_genes_out):
     100            self.logger.warning( \
    100101                            ("Number of genes after gene join (%i) does not " +
    101102                            "match the number of genes of the input (%i).") \
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