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  • 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/core/sequence.py
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from operator import eq, ne
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from random import shuffle
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import re
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import logging
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LOG = logging.getLogger('cogent.data')
 
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import warnings
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__author__ = "Rob Knight, Gavin Huttley, and Peter Maxwell"
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__copyright__ = "Copyright 2007-2009, The Cogent Project"
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__credits__ = ["Rob Knight", "Peter Maxwell", "Gavin Huttley",
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                    "Matthew Wakefield", "Daniel McDonald"]
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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__ = "Rob Knight"
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__email__ = "rob@spot.colorado.edu"
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__status__ = "Production"
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    def gettype(self):
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        """Return the sequence type."""
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        return self.MolType._type
 
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        return self.MolType.label
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    def resolveambiguities(self):
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        """Returns a list of tuples of strings."""
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        ambigs = self.MolType.resolveAmbiguity
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        return [ambigs(motif) for motif in self._seq]
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    def slidingWindows(self, window, step):
 
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    def slidingWindows(self, window, step, start=None, end=None):
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        """Generator function that yield new sequence objects
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        of a given length at a given interval.
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        Arguments:
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            - window: The length of the returned sequence
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            - step: The interval between the start of the returned
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              sequence objects"""
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        for pos in range(0, len(self)-window+1,step):
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            yield self[pos:pos+window]
 
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              sequence objects
 
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            - start: first window start position
 
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            - end: last window start position
 
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        """
 
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        start = [start, 0][start is None]
 
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        end = [end, len(self)-window+1][end is None]
 
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        end = min(len(self)-window+1, end)
 
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        if start < end and len(self)-end >= window-1:
 
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            for pos in xrange(start, end, step):
 
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                yield self[pos:pos+window]
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    def getInMotifSize(self, motif_length=1, log_warnings=True):
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        """returns sequence as list of non-overlapping motifs
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            length = len(seq)
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            remainder = length % motif_length
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            if remainder and log_warnings:
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                LOG.warning('Dropped remainder "%s" from end of sequence' %
 
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                warnings.warn('Dropped remainder "%s" from end of sequence' %
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                        seq[-remainder:])
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            return [seq[i:i+motif_length]
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                    for i in range(0, length-remainder, motif_length)]