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# Changelog

## Cogent 1.4.1 - 1.5

### 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

## Cogent 1.4 - 1.4.1

### 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

## Cogent 1.3 - 1.4

### New Features

- added support for manipulating and handling macromolecular structures. This includes a PDB file format parser, a hierarchical data structure to represent molecules. Various utilities to manipulate e.g. clean-up molecules, efficient surface area and proximity-contact calculation via cython. Expansion into unit-cells and crystal lattices is also possible.
- added a KD-Tree class for fast nearest neighbor look-ups. Supports k-nearest neighbours and all neighbours within radius queries currently only in 3D.
- added new tools for evaluating clustering stresses, goodness_of_fit. In cogent.cluster .
- added a new clustering tool, procrustes analysis. In cogent.cluster .
- phylo.distance.EstimateDistances class has a new argument, modify_lf. This allows the use the modify the likelihood function, possibly constraining parameters, freeing them, setting bounds, pre-optimising etc..
- cogent Table mods; added transposed and normalized methods while the summed method can now return column or row sums.
- Added a new context dependent model class. The conditional nucleotide frequency weighted class has been demonstrated to be superior to the model forms of Goldman and Yang (1994) and Muse and Gaut (1994). The publication supporting this claim is In press at Mol Biol Evol, authored by Yap, Lindsay, Easteal and Huttley.
- added new argument to LoadTable to facilitate speedier loading of large files. The static_column_types argument auto-generates a separator format parser with column conversion for numeric columns.
- added BLAST XML parser + tests.
- Add compatibility matrix module for determining reticulate evolution.
- Added ‘start’ and ‘order’ options to the WLS and ML tree finding method .trex() These allow the search of tree-space to be constrained to start at a particular subtree and to proceed in a specified order of leaf additions.
- Consensus tree of weighted trees from phylo.maximum_likelihood.
- Add Alignment.withGapsFrom() aka mirrorGaps, mirrors the gaps into a provided alignment.
- added ANOVA to maths.stats.test
- LoadTable gets an optional argument (static_column_types) to simplify speedy loading of big files.

### Changes

- Python 2.4 is no longer supported.
- NumPy 1.3 is now the minimum supported NumPy version.
- zlib is now a dependency.
- cogent.format.table.asReportlabTable is being discontinued in version 1.5. This is the last dependency on reportlab and removal will simplify installation.
- the conditional nucleotide model (Yap et al 2009) will be made the default model form for context dependent models in version 1.5.
- Change required MPI library from PyxMPI to mpi4py.
- Move all of the cogent.draw.matplotlib.* modules up to cogent.draw.*
- Substitute matplotlib for reportlab throughout cogent.draw
- cogent.db.ensembl code updated to work with the latest Ensembl release (56)
- motif prob pseudocount option, used for initial values of optimisable mprobs
- The mlagan application controller has been removed.

### Bug Fixes

- Fix and test for two bugs in multiple alignment, One in the pairwise.py Hirschberg code and the other in indel_positions.py where gaps at the end were effectively taken to be deletions and never insertions, unlike gaps at the start.
- fix #2811993 alignment getMotifProbs. allow_gap argument now has an effect.

## Cogent 1.2 - 1.3

### New Features

- Python2.6 is now supported
- added cogent.cluster.nmds, code to perform nonmetric multidimensional scaling. Not as fast as others (e.g.: R, MASS package, isoMDS)
- Documentation ported to using the Sphinx documentation generator.
- Major additions to documentation in doc/examples.
- Added partial support for querying the Ensembl MySQL databases. This capacity has additional dependencies (MySQL-python and SQLAlchemy). This module should be considered alpha level code, (although it has worked reliably for some time in the hands of the developers).
- Introduced a new substitution model family. This family has the same form as that originally described by Muse and Gaut (Mol Biol Evol, 11, 715-24). These models were applied in the article by Lindsay et al. (2008, Biol Direct, 3, 52). Model state defaults to the tuple weighted matrix (eg. the Goldman and Yang codon models). Selecting the nucleotide weighted matrix is done using the mprob_model argument.
- Likelihood functions now have a getStatistics method. This returns cogent Table objects. Optional arguments are with_motif_probs and with_titles where the latter refers to the Table.Title attribute being set.
- Added rna_struct formatter and rna_plot parser
- A fast unifrac method implementation.
- Added new methods on tree related objects: TreeNode.getNodesDict; TreeNode.reassignNames; PhyloNode.tipsWithinDistance; PhyloNode.totalDescendingBranchLength
- Adopted Sphinx documentation system, added many new use cases, improved existing ones.
- added setTablesFormat to likelihood function. This allows setting the spacing, display precision of the stats tables resulting from printing a likelihood function.
- Added non-parametric multidimensional scaling (nmds) method.
- Added a seperate app controller for FastTree v1.0
- new protein MolType, PROTEIN_WITH_STOP, that supports the stop codon new sequence objects, ProteinWithStopSequence and ModelProteinWithStopSequence to support the new MolType.
- Support for Cython added.

### Changes

- reconstructAncestralSequences has been deprecated to reconstructAncestralSeqs. It will be removed in version 1.4.
- updated parsers
- TreeNode.getNewick is now iterative. For recursive, use TreeNode.getNewickRecursive. Both the iterative and recursive methods of getNewick now support the keyword ‘escape_name’. DndParser now supports the keyword ‘unescape_name’. DndParser unescape_name will now try to remove underscores (like underscore_unmunge).
- Generalized MinimalRnaalifoldParser to parse structures and energies from RNAfold as well.
- PhyloNode.tipToTipDistances can now work on a subset of tips by passing either a list of tip names or a list of tip nodes using the endpoints param.
- deprecating reconstructAncestralSequences to deprecating reconstructAncestralSeqs.
- updated app controller parameters for FastTree v1.1
- Allow and require a more recent version of Pyrex.
- LoadTree is now a method of cogent.__init__

Warning

Pyrex is no longer the accepted way to develop extensions. Use Cython instead.

### Bug Fixes

- the alignment sample methods and xsample (randint had the wrong max argument)
- Fixes the tests that no longer work with NCBI’s API changes, and sticks a big warning for the unwary in the ncbi module pointing users to the “official” list of reported rettypes. Note that the rettypes changed recently and NCBI says they do not plan to support the old behavior.
- The TreeNode operators cmp, contains, and any operator that relies on those methods will now only perform comparisons against the objects id. Prior behavior first checked the TreeNode’s Name attribute and then object id if the Name was not present. This resulted in ambiguous behavior in certain situations.
- Added type conversion to Mantel so it works on lists.
- kendall tau fix, bug 2794469
- Table now raises a RuntimeError if provided malformed data.
- Fixed silent type conversion in TreeNode, bug 2804431
- RangeNode is now properly passing kwargs to baseclass, bug 2804441
- DndParser was not producing correct trees in niche cases, bug 2798580

## Cogent 1.1 - 1.2

### New Features

- Code for performing molecular coevolution/covariation analyses on multiple sequence alignments, plus support files. (Described in J. Caporaso et al. BMC Evol Biol, 8(1):327, 2008.)
- App controller for CD-HIT
- A ParameterEnumerator object is now available in cogent.app.util. This method will iterate over a range of parameters, returning parameter dicts that can be used with the relevant app controller.
- Sequence and alignment objects that inherit from Annotatable can now mask regions of sequence, returning new objects where the observed sequence characters in the regions spanned by the annotations are replaced by a mask character (mask_char).
- Table.count method. Counts the number of rows satisfying some condition.
- Format writer for stockholm and clustal formats.
- App controllers for dotur, infernal, RNAplot, RNAalifold. Parsers for infernal and dotur.
- Empirical nucleotide substitution matrix estimation code (Described in M. Oscamou et al. BMC Bioinformatics, 9(1):511, 2008)

### New Documentation

Usage examples (see doc/) were added for the following:

- Querying NCBI
- The motif module.
- UPGMA clustering
- For using the ParameterCombinations object and generating command lines
- Coevolution modelling
- Sequence annotation handling
- Table manipulation
- Principal components analysis (PCoA)
- Genetic code objects
- How to construct profiles, consensus seqs etc ..

### Changes

- PyCogent no longer relies on the Python math module. All math functions are now imported from numpy. The main motivator was to remove casting between numpy and Python types. Such as, a ‘numpy.float64’ variable unknowingly being converted to a Python ‘float’ type.
- Tables.getDistinctValues now handles multiple columns.
- Table.Header is now an immutable property of Tables. Use the withNewHeader method modifying Header labels.
- The TreeNode comparison methods now only check against the objects ID

### Bug Fixes

- LoadTable was ignoring title argument for standard file read.
- Fixed bug in Table.joined. When a join produces no result, now returns a Table with 0 rows.
- Improved consistency of LoadTable with previous behaviour of cogent.Table
- Added methods to detect large sequences/alphabets and handle counts from sequence triples correctly.
- goldman_q_dna_pair() and goldman_q_rna_pair() now average the frequency matrix used.
- reverse complement of annotations with disjoint spans correctly preserve order.
- Fixed ambiguity in TreeNode comparison methods which resulted in the prune method incorrectly removing entire subtrees.

## Cogent 1.0.1 - 1.1

### New Features

- Added functionality to cogent.util.unit_test.TestCase

    assertSameObj - use in place of ‘assert a is b’ assertNotSameObj - use in place of ‘assert a is not b’ assertIsPermutation - checks if observed is a permutation of items assertIsProb - checks whether a value(s) are probabilities assertIsBetween - use in place of ‘assert a < obs < b’ assertLessThan - use in place of ‘assert obs < value’ assertGreaterThan - use in place of ‘assert obs > value’ assertSimiliarFreqs - compares frequency distributions using a G-test assertSimiliarMeans - compares samples using a t-test _set_suite_pvalue - set a suite wide pvalue

    Note

    both the similiarity assertions can have a pvalue specified in the testing module. This pvalue can be overwritten during alltests.py by calling TestCase._set_suite_pvalue(pvalue)

    Note

    All of these new assert methods can take lists as well. For instance: obs = [1,2,3,4] value = 5 self.assertLessThan(obs, value)

- Alignment constructor now checks for iterators (e.g. results from parsers) and lists() them – this allows direct construction like Alignment(MinimalFastaParser(open(myfile.fasta))). Applies to both dense and sparse alignments, and SequenceCollections.

- Parameterized LoadTree underscore stripping in node names, and turned it off by default.

- new Table features and refactor

    Trivial edits of the code provided by Felix Schill for SQL-like table joining. Principally a unification of the different types of table joins (inner- and outer-join) between 2 tables, and porting of all testing code into test_table.rest. The method Table.joined provides the interface (see tests/test_table.rest for usage).

- added a Table.count method

    simply counts the number of rows satisfying some condition. Method has the same args as for Table.filtered.

- Functions for obtaining the rate matrix for 2 or 3 sequences using the Goldman method. Support for RNA and DNA.

- Additions to clustalw and muscle app controllers
    muscle.py

      add_seqs_to_alignment align_two_alignments align_unaligned_seqs align_and_build_tree build_tree_from_alignment

    clustalw.py

      align_unaligned_seqs bootstrap_tree_from_alignment build_tree_from_alignment align_and_build_tree

- App controllers for Clearcut, ClustalW, Mafft

- Added midpoint rooting

- Accept FloatingPointError as well as ZeroDivisionError to accommodate numpy.

- Trees can now compare themselves to other trees using a couple of methods.

    subsets: compare based on fraction of subsets of labels defined by clades that are the same in the two trees.

    tip_to_tip: compare based on correlations of tip_to_tip distances.

    Both of these are fairly badly behaved statistically, so should always be compared to a distribution of values from random (e.g. label-permuted) trees using Monte Carlo.

- Added ability to exclude non-shared taxa from subsets tree cmp method.

- Added Zongzhi’s combination and permutation implementations to transform.py.

- Added some docs to UPGMA_cluster.

- Added median in cogent.maths.stats.test Added because the numpy version does not support an axis parameter. This function now works like numpy functions (sum, mean, etc...) where you can specify axis. This function should be safe in place of numpy.median.

### Changes

- Many changes to the core objects, mainly for compatibility. Major changes in this update:

  > - ModelSequence now inherits from SequenceI and supports the various Sequence methods (e.g. nucleic acids can reverse-complement, etc.). Type checking is still performed using strings (e.g. for ambiguous characters, etc.) and could be improved, but everything seems to work. Bug # 1851959.
  > - ModelProteinSequence added. Bug # 1851961.
  > - DenseAlignment and ModelSequence can now handle the ‘?’ character, which is added to the Alphabet during install. Bug # 1851483.
  > - Fixed a severe bug in moltype constructors that mutated the dict of ambiguous states after construction of each of the standard moltypes (for example, preventing re-instantiation of a similar moltype after the initial install: bug # 1851482. This would have been very confusing for anyone trying to experiment with custom MolTypes.
  > - DenseAlignment now implements many methods of Alignment (some of which have actually been moved into SequenceCollection), e.g. getGappedSeq() as per bug # 1816573.

- Added parameter to MageListFromString and MageGroupFromString. Can now handle ‘on’ as well as ‘off’.

- SequenceCollection, Alignment, etc. now check for duplicate seq labels and raise exception or strip duplicates as desired. Added unit test to cover this case.

  > - SequenceCollection now also produces FASTA as default __str__ behavior like the other objects.
  > - DenseAlignment now iterates over its mapped items, not the indices for those items, by default. This allows API compatibility with Alignment but is slow: it may be worth optimizing this for cases such as detecting ambiguous chars, as I have already implemented for gaps.

- Updated std in cogent.maths.stats.test

  > - std now takes an axis parameter like numpy functions (sum, mean,etc...).

  > - also added in a docstring and tests.

  >     Note

  >     cogent.maths.stats.test import sqrt from numpy instead of math in order to allow std to work on arrays.

- Tree now uses iterative implementation of traverse().

    Warning

    If you do modify the tree while using traverse(), you will get undesired results. If you need to modify the tree, use traverse_recursive() instead. This only applies to the tree topology (e.g. if you are adding or deleting nodes, or moving nodes around; doesn’t apply if you are changing branch lengths, etc.). The only two uses I found in Cogent where the tree is modified during iteration are in rna2d (some of the structure tree operations) and the prune() method. I have changed both to use traverse_recursive for now. However, there might be issues with other code. It might be worth figuring out how to make the iterative method do the right thing when the tree is modified – suggestions are welcome provided they do not impose substantial performance penalties.

- Made compatible with Python 2.4

- Changed dev status in setup call

- Dropping comments indicating windows support

### Bug Fixes

- Fixed bug 1850981: UPGMA does not check diagonals.

    This bug was caused because the UPGMA algorithm picks the smallest distances between nodes at each step but should not ever pick something on the diagonal. To prevent a diagonal choice we set it to a large number, but sometimes, for very large matrices, the diagonal sometimes is chosen becuase the number decreases in value as the distances are averaged during node collapse. To prevent this error, the program now checks to make sure that the selected smallest_index is not on the diagonal. If it is, it reassigns the diagonal to the large number.

- Fixed bug in gff.py attribute string parsing.

    If attribute string did not contain double quotes, find() returned -1, so the last character of the string was inadvertently omitted.

- Fixed error in taxonomy convenience functions that failed to pass in the specified database.

    This used to be masked by ncbi’s automatic conversion between protein and nucleotide ids, but apparently this conversion no longer operates in the tested cases.

- fixed unittest methods

    Zongzhi noticed that assertFloatEqual would compare two against when a shape (4,0) array was compared against a shape (4,4) array. I added tests for assertFloatEqual, assertFloatEqualAbs, assertFloatEqualRel and assertEqual. The same bug was noticed in assertFloatEqualRel. They are now fixed. These fixes resulted in errors in maths.stats.test.std and correlation_matrix. The std function needed a work over, but the correlation_matrix was a fault in the test case itself.

- fixed bug in reading tab-delimited tables

    failure when a record had a missing observation in the last field has been fixed. Line stripping of only line-feed characters is now done.

- Fixed important bug in metric_scaling.

    numpy eig() produces eigenvector array that is the transpose of Numeric eig(). Therefore, any code that does not take this into account will produce results that are TOTALLY INCORRECT when fed to downstream analyses. Coordinates from this module prior to this patch are incorrect and are not to be trusted.

- Fixed a typo in dialign test

- tree __repr__ now more robust to non-str Name entries

- seqsim.rangenode traverse now compatible /w base class.

- Fixed line color bug in PR2 bias plots.

- Added method to dump raw coords from dendrogram.

- Fixed called to eigenvector when no pyrex

- Fixed bug in nonrecursive postorder traversal if not root

## Cogent 1.0 - (9/8/2007)

- Initial release

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