Cogent

==================

NOTE: There have been so many changes since the 1.5.3 release that it is not
viable to list themn all! Suffice it to say, many new features added and many bugs
have been squashed. The best way to see them is using either git or mercurial
to examine the commit logs.

====================

New Features
------------

* Added a withoutLostSpans() method to Feature objects in
cogent.core.annotation. Useful after projecting features from one aligned
sequence across to another. Implemented for ordinary Features and
SimpleVariables but not xxy_list Variables.

Changes
-------

* Make Span.remapWith() a little clearer in cogent.core.location.
* Tidy annotation remapping code in cogent.core.annotation and
cogent.core.sequence so that new positions are only calculated once when
slicing, projecting, or otherwise remapping parts of sequences. The old code
was needlessly doing it twice.

Bug Fixes
---------

* Fixed bug in BLAT application controller (cogent.app.blat) which would drop
some input sequences when running assign_dna_reads_to_protein_database.
* Prevent negative widths from arising in cogent.draw.compatibility when
alignment is too wide.

====================

New Features
------------

* Added new mantel_test function to cogent.maths.stats.test that allows the
type of significance test to be specified. This function is meant to replace
the pre-existing mantel function.
* Added new correlation_test function to cogent.maths.stats.test that computes
the correlation (pearson or spearman) between two vectors, in addition to
parametric and nonparametric tests of significance and confidence intervals.
This function gives more control and information than the pre-existing
correlation function. The spearman function is also a new addition.
* Added new mc_t_two_sample function to cogent.maths.stats.test that performs a
two-sample t-test and uses Monte Carlo permutations to determine
nonparametric significance (similar to R's Deducer::perm.t.test).
* Added guppy 1.1, pplacer 1.1, ParsInsert 1.04, usearch 5.2.32, rtax 0.981,
raxml 7.3.0, BLAT 34, and BWA 0.6.2 application controllers.
* Added new functions to cogent.maths.stats.rarefaction that provide
alternative ways to perform rarefaction subsampling.
* Added convenience wrappers assign_dna_reads_to_database,
assign_dna_reads_to_protein_database, and assign_dna_reads_to_dna_database
for BLAT, BWA, and usearch with consistent interface across all three.

Changes
-------

* Minimum matplotlib version now set to 1.1.0.
* Minimum Vienna package version now set to 1.8.5.
* The pearson function in cogent.maths.stats.test has more robust
error-checking.
* The mantel and mantel_test functions in cogent.maths.stats.test now check for
symmetric, hollow distance matrices as input by default, with an option to
disable these checks.
* cogent.draw.distribution_plots now uses matplotlib proxy Artists for legend
creation (this simplifies the code a bit). Added ability to set the size of
plot figures through two new optional parameters to generate_box_plots and
generate_comparative_plots. More robust checks have been put in place in
case making room for labels fails (this now uses matplotlib 1.1.0's new
tight_layout() functionality, but this can still fail in some cases).
* cogent.app.raxml (version 7.0.3) is now deprecated and will be removed in
1.6.0. Please use cogent.app.raxml_v730 instead (version 7.3.0).
* cogent.app.muscle (version 3.6) is now deprecated and will be removed in
1.6.0. Please use cogent.app.muscle_v38 instead (version 3.8).
* Updated cogent.app.uclust to handle --stepwords and --w.

Bug Fixes
---------

* improve handling of reading frames from Ensembl
* actually included the test_ensembl/test_metazoa.py file that was
accidentally overlooked.
* fixed small diff in postcript output from RNAfold
* Deprecation and discontinued warnings are now not ignored by default.
cogent.util.warning was ignored in Python 2.7 because it uses
DeprecationWarnings. These warnings are temporarily forced to not be ignored.
* Included test_app/test_formatdb.py and test_app/test_mothur.py files in
alltests.py.
* Fixed test_safe_md5 in tests.test_util.test_misc to no longer run an MD5 over
a file in PyCogent (this caused the test to break when a new release went out
because the MD5 changes due to the new version string). The test now writes a
temporary file populated with fixed data and computes the MD5 from that.
* Fixed data_file_links.html in the PyCogent documentation to correctly point
to several data files that were previously unreachable.

==================

New Features
------------

* Alignments can now add sequences that are pairwise aligned to a sequence
already present in the alignment.
* Alignment.addSeqs has more flexibility with the specific order of sequences
now controllable by the user. Thanks to Jan Kosinski for these two very
useful patches!
* Increased options for reading Table data from files: limit keyword; and,
line based (as distinct from column-based) type-casting of delimited files.
* Flexible parser for raw Greengenes 16S records
* Add fast pairwise distance estimation for DNA/RNA sequences. Currently only
Jukes-Cantor 1969 and Tamura-Nei 1993 distances are provided. A cookbook
entry was added to building_phylogenies.
* Added a PredefinedNucleotide substitution model class. This class uses
Cython implementations for nucleotide models where analytical solutions
are available. Substantial speedups are achieved. These implementations
do not support obtaining the rate matrix. Use the older style implementation
if you require that (toggled by the rate_matrix_required argument).
* Added fit_function function. This allows to fit any model to a x and y
dataset using simplex to reduce the error between the model and the data.
* Added parsers for bowtie and for BLAT's PSL format
* Table can now read/write gzipped files.
* GeneticCode class has a getStopIndices method. Returns the index positions
of stop codons in a sequence for a user specified translation frame.
* Added LogDet metric to cogent.evolve.pairwise_distance. With able assistance
from Yicheng Zhu. Thanks Yicheng!
* Added jackknife code to cogent.maths.stats.jackknife. This can be used to
measure confidence of an estimate from a single vector or a matrix. Thanks
to Anuj Pahwa for help implementing this!
* Added abundance-based Jaccard beta diversity index (Chao et. al., 2005)

Changes
-------

* python 2.6 is now the minimum required version
* We have removed code authored by Ziheng Yang as it is not available under
an open source license. We note a modest performance hit for nucleotide and
dinucleotide models. Codon models are not affected. The PredefinedNucleotide
models recently added are faster than the older approach that used Yang's
code.
* The PredefinedNucleotide models are now available via cogent.evolve.models.
The old-style (slower) nucleotide models can be obtained by setting
rate_matrix_required=True.
* RichGenbankParser can now return WGS blocks

Bug Fixes
---------

* fixed bug that crept into doing consensus trees from tree collections.
Thanks to Klara Verbyla for catching this one!
* fixed a bug (3170464) affecting obtaining sequences from non-chromosome
level coordinate systems. Thanks to brandoninvergo for reporting and Hua
Ying for the patch!
* fixed a bug (2987278) associated with missing unit tests for gbseq.py
* fixed a bug (2987264) associated with missing unit tests for paml_matrix.py
* fixed a bug (2987238) associated with missing unit tests for tinyseq.py

==================

New Features
------------

* major additions to Cookbook. Thanks to the many contributors (too many to
list here)!
* added AlleleFreqs attribute to ensembl Variation objects.
* added getGeneByStableId method to genome objects.
* added Introns attribute to Transcript objects and an Intron class. (Thanks
to Hua Ying for this patch!)
* 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

Changes
-------

* thousand fold performance improvement to nmds
* >10-fold performance improvements to some Table operations

Bug Fixes
---------

* Fixed a Bug in cogent.core.alphabet that resulted in 4 tests err'ing out
when using NumPy v1.4.1
* Sourceforge bugs 2987289, 2987277, 2987378, 2987272, 2987269 were addressed
and fixed

==================

New Features
------------

* Simplified getting genetic variation from Ensembl and provide the protein
location of nonsynonymous variants.
* rate heterogeneity variants of pre-canned continuous time substitution
models easier to define.
* Added implementation of generalised neighbour joining.
* New capabilities for examining genetic variants using Ensembl.
* Phylogenetic methods that can return collections of trees do so as a
TreeCollections object, which has writeToFile and getConsensusTree methods.
* Added uclust application controller which currently supports uclust
v1.1.579.

Changes
-------

* Major additions to Cookbook documentation courtesy of Tom Elliot. Thanks
Tom!
* Improvements to parallelisation.

Bug Fixes
---------