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Viewing changes to cogent/evolve/likelihood_tree.py

  • Committer: Bazaar Package Importer
  • Author(s): Steffen Moeller
  • Date: 2010-12-04 22:30:35 UTC
  • mfrom: (1.1.1 upstream)
  • Revision ID: james.westby@ubuntu.com-20101204223035-j11kinhcrrdgg2p2
Tags: 1.5-1
* Bumped standard to 3.9.1, no changes required.
* New upstream version.
  - major additions to Cookbook
  - added AlleleFreqs attribute to ensembl Variation objects.
  - added getGeneByStableId method to genome objects.
  - added Introns attribute to Transcript objects and an Intron class.
  - added Mann-Whitney test and a Monte-Carlo version
  - exploratory and confirmatory period estimation techniques (suitable for
    symbolic and continuous data)
  - Information theoretic measures (AIC and BIC) added
  - drawing of trees with collapsed nodes
  - progress display indicator support for terminal and GUI apps
  - added parser for illumina HiSeq2000 and GAiix sequence files as 
    cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
  - added parser to FASTQ files, one of the output options for illumina's
    workflow, also added cookbook demo.
  - added functionality for parsing of SFF files without the Roche tools in
    cogent.parse.binary_sff
  - thousand fold performance improvement to nmds
  - >10-fold performance improvements to some Table operations

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cogent/evolve/likelihood_tree.py
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numpy.seterr(all='ignore')
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import logging
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numerictypes = numpy.core.numerictypes.sctype2char
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LOG = logging.getLogger('cogent')
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__author__ = "Peter Maxwell"
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
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__credits__ = ["Peter Maxwell", "Rob Knight"]
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__license__ = "GPL"
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__version__ = "1.4.1"
 
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__version__ = "1.5.0"
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__maintainer__ = "Peter Maxwell"
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__email__ = "pm67nz@gmail.com"
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__status__ = "Production"
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try:
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    pyrex = importVersionedModule('_likelihood_tree', globals(), 
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            (2, 1), LOG, "pure Python/NumPy likelihood tree")
 
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            (2, 1), "pure Python/NumPy likelihood tree")
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except ExpectedImportError:
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    pyrex = None
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                        u = len(c.uniq)-1 # gap
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                    else:
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                        u = c.index[col]
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                        if not ( 0 <= u < len(c.uniq)-1):
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                            print len(c.uniq)
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                            print c.uniq[-1]
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                            print align_index
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                            raise RuntimeError
 
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                        assert 0 <= u < len(c.uniq)-1, (
 
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                                u, len(c.uniq), c.uniq[-1], align_index)
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                    a.append(u)
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                assignments.append(a)
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        (uniq, counts, self.index) = _indexed(zip(*assignments))