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Committer:
Bazaar Package Importer
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Author(s):
Steffen Moeller
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Date:
2010-12-04 22:30:35 UTC
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mfrom:
(1.1.1 upstream)
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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