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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/app/infernal.py
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#!/usr/bin/env python
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"""
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Provides an application controller for the commandline version of:
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Infernal 1.0
 
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Infernal 1.0 and 1.0.2 only.
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"""
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from cogent.app.parameters import FlagParameter, ValuedParameter, FilePath
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from cogent.app.util import CommandLineApplication, ResultPath, get_tmp_filename
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__copyright__ = "Copyright 2007-2009 2007, The Cogent Project"
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__credits__ = ["Jeremy Widmann"]
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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__ = "Jeremy Widmann"
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__email__ = "jeremy.widmann@colorado.edu"
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__status__ = "Development"
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    res = app(paths)
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    search_results = list(CmsearchParser(res['SearchResults'].readlines()))
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    if search_results:
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        for i,line in enumerate(search_results):
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            label = line[0]
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            search_results[i][0]=int_keys.get(label,label)
 
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            label = line[1]
 
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            search_results[i][1]=int_keys.get(label,label)
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    res.cleanUp()
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    for f in to_remove:remove(f)
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    if search_results:    
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        for i,line in enumerate(search_results):
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            label = line[0]
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            search_results[i][0]=int_keys.get(label,label)
 
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            label = line[1]
 
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            search_results[i][1]=int_keys.get(label,label)
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    res.cleanUp()
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