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Viewing changes to Bio/Blast/NCBIXML.py

  • Committer: Bazaar Package Importer
  • Author(s): Philipp Benner
  • Date: 2009-08-24 09:29:27 UTC
  • mfrom: (1.3.3 upstream) (4.1.4 sid)
  • Revision ID: james.westby@ubuntu.com-20090824092927-2wwh36vwnfgn98kl
Tags: 1.51final-2
http://bugs.debian.org/543236
Merged patch from ubuntu to make the package ready for
python2.6 (Closes: #543236).

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Lines of Context:
Bio/Blast/NCBIXML.py
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                    print "NCBIXML: Ignored: " + method
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                self._debug_ignore_list.append(method)
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        #We don't care about white space in parent tags like Hsp,
 
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        #but that white space doesn't belong to child tags like Hsp_midline
 
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        if self._value.strip() :
 
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            raise ValueError("What should we do with %s before the %s tag?" \
 
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                             % (repr(self._value), name))
 
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        self._value = ""
 
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    def characters(self, ch):
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        """Found some text
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        name -- tag name
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        """
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        # Strip character buffer
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        self._value = self._value.strip()
 
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        # DON'T strip any white space, we may need it e.g. the hsp-midline
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        # Try to call a method (defined in subclasses)
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        method = self._secure_name('_end_' + name)
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    def _end_Hsp_midline(self):
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        """Formatting middle line as normally seen in BLAST report
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        """
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        self._hsp.match = self._value
 
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        self._hsp.match = self._value # do NOT strip spaces!
 
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        assert len(self._hsp.match)==len(self._hsp.query)
 
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        assert len(self._hsp.match)==len(self._hsp.sbjct)
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    # Statistics
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    def _end_Statistics_db_num(self):