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scikit-bio changelog

Version 0.4.0-dev (changes since 0.4.0 release go here)

Features

  • Added skbio.io.format.blast7 for reading BLAST+ output format 7 or BLAST output format 9 files into a pd.DataFrame. (#1110)
  • Added skbio.stats.composition.ancom function, a test for differential abundance #1054
  • Added skbio.DissimilarityMatrix.to_data_frame method for creating a pandas.DataFrame from a DissimilarityMatrix or DistanceMatrix. (#757)
  • Added support for one-dimensional vector of dissimilarities in skbio.stats.distance.DissimilarityMatrix constructor. (#6240)
  • Added skbio.io.format.blast6 for reading BLAST+ output format 6 or BLAST output format 8 files into a pd.DataFrame. (#1110)
  • Added inner, ilr, ilr_inv and clr_inv, skbio.stats.composition, which enables linear transformations on compositions (#892
  • Added skbio.diversity.alpha.pielou_e function as an evenness metric of alpha diversity. (#1068)
  • Added to_regex method to skbio.sequence._iupac_sequence ABC - it returns a regex object that matches all non-degenerate versions of the sequence.
  • Added skbio.util.assert_ordination_results_equal function for comparing OrdinationResults objects in unit tests.
  • Added skbio.io.format.genbank for reading and writing GenBank/GenPept for DNA, RNA, Protein and Sequence classes.
  • Added skbio.util.RepresentationWarning for warning about substitutions, assumptions, or particular alterations that were made for the successful completion of a process.
  • TreeNode.tip_tip_distances now supports nodes without an associated length. In this case, a length of 0.0 is assumed and an skbio.util.RepresentationWarning is raised. Previous behavior was to raise a NoLengthError. (#791)
  • DistanceMatrix now has a new constructor method called from_iterable.
  • Sequence now accepts lowercase keyword like DNA and others. Updated fasta, fastq, and qseq readers/writers for Sequence to reflect this.
  • The lowercase method has been moved up to Sequence meaning all sequence objects now have a lowercase method.
  • Added phylogenetic diversity metrics, including weighted UniFrac, unweighted UniFrac, and Faith's Phylogenetic Diversity. These are accessible as skbio.diversity.beta.unweighted_unifrac, skbio.diversity.beta.weighted_unifrac, and skbio.diversity.alpha.faith_pd, respectively.
  • Added reverse_transcribe class method to RNA.
  • Added Sequence.observed_chars property for obtaining the set of observed characters in a sequence. (#1075)
  • Added Sequence.frequencies method for computing character frequencies in a sequence. (#1074)
  • Added experimental class-method Sequence.concat which will produce a new sequence from an iterable of existing sequences. Parameters control how positional metadata is propagated during a concatenation.
  • Added phylogenetic diversity metrics, including weighted UniFrac, unweighted UniFrac, and Faith's Phylogenetic Diversity. These are accessible as skbio.diversity.beta.unweighted_unifrac, skbio.diversity.beta.weighted_unifrac, and ````skbio.diversity.alpha.faith_pd``, respectively.
  • Addition of the function skbio.diversity.alpha_diversity to support applying an alpha diversity metric to multiple samples in one call.
  • Addition of the functions skbio.diversity.get_alpha_diversity_metrics and skbio.diversity.get_beta_diversity_metrics to support discovery of the alpha and beta diversity metrics implemented in scikit-bio.
  • TreeNode.to_array now supports replacing nan branch lengths in the resulting branch length vector with the value provided as nan_length_value.
  • skbio.io.format.phylip now supports sniffing and reading strict, sequential PHYLIP-formatted files into skbio.Alignment objects. (#1006)
  • Added default_gap_char class property to DNA, RNA, and Protein for representing gap characters in a new sequence.

Backward-incompatible changes [stable]

  • Sequence.kmer_frequencies now returns a dict. Previous behavior was to return a collections.Counter if relative=False was passed, and a collections.defaultdict if relative=True was passed. In the case of a missing key, the Counter would return 0 and the defaultdict would return 0.0. Because the return type is now always a dict, attempting to access a missing key will raise a KeyError. This change may break backwards-compatibility depending on how the Counter/defaultdict is being used. We hope that in most cases this change will not break backwards-compatibility because both Counter and defaultdict are dict subclasses.

    If the previous behavior is desired, convert the dict into a Counter/defaultdict:

    import collections
from skbio import Sequence
seq = Sequence('ACCGAGTTTAACCGAATA')

# Counter
freqs_dict = seq.kmer_frequencies(k=8)
freqs_counter = collections.Counter(freqs_dict)

# defaultdict
freqs_dict = seq.kmer_frequencies(k=8, relative=True)
freqs_default_dict = collections.defaultdict(float, freqs_dict)

    Rationale: We believe it is safer to return dict instead of Counter/defaultdict as this may prevent error-prone usage of the return value. Previous behavior allowed accessing missing kmers, returning 0 or 0.0 depending on the relative parameter. This is convenient in many cases but also potentially misleading. For example, consider the following code:

    from skbio import Sequence
seq = Sequence('ACCGAGTTTAACCGAATA')
freqs = seq.kmer_frequencies(k=8)
freqs['ACCGA']

    Previous behavior would return 0 because the kmer 'ACCGA' is not present in the Counter. In one respect this is the correct answer because we asked for kmers of length 8; 'ACCGA' is a different length so it is not included in the results. However, we believe it is safer to avoid this implicit behavior in case the user assumes there are no 'ACCGA' kmers in the sequence (which there are!). A KeyError in this case is more explicit and forces the user to consider their query. Returning a dict will also be consistent with Sequence.frequencies.

Backward-incompatible changes [experimental]

  • Replaced PCoA, CCA, CA and RDA in skbio.stats.ordination with equivalent functions pcoa, cca, ca and rda. These functions now take pd.DataFrame objects.
  • Change OrdinationResults to have its attributes based on pd.DataFrame and pd.Series objects, instead of pairs of identifiers and values. The changes are as follows:
    • species and species_ids have been replaced by a pd.DataFrame named features.
    • site and site_ids have been replaced by a pd.DataFrame named samples.
    • eigvals is now a pd.Series object.
    • proportion_explained is now a pd.Series object.
    • biplot is now a pd.DataFrame object named biplot_scores.
    • site_constraints is now a pd.DataFrame object named sample_constraints.
  • short_method_name and long_method_name are now required arguments of the OrdinationResults object.
  • Removed skbio.diversity.alpha.equitability. Please use skbio.diversity.alpha.pielou_e, which is more accurately named and better documented. Note that equitability by default used logarithm base 2 while pielou_e uses logarithm base e as described in Heip 1974.
  • skbio.diversity.beta.pw_distances is now called skbio.diversity.beta_diversity. This function no longer defines a default metric, and metric is now the first argument to this function.
  • Deprecated function skbio.diversity.beta.pw_distances_from_table has been removed from scikit-bio, as scheduled. Code that used this should be adapted to use skbio.diversity.beta_diversity.
  • TreeNode.index_tree now returns a 2-D numpy array as its second return value (the child node index) instead of a 1-D numpy array.

Bug Fixes

  • Sequence objects now handle slicing of empty positional metadata correctly. Any metadata that is empty will no longer be propagated by the internal _to constructor. (#1133)
  • DissimilarityMatrix.plot() no longer leaves a white border around the heatmap it plots (PR #1070).

Deprecated functionality [stable]

  • skbio.Sequence.copy has been deprecated in favor of copy.copy(seq) and copy.deepcopy(seq).

Deprecated functionality [experimental]

  • SequenceCollection.distances has been deprecated in favor of DistanceMatrix.from_iterable. Use key="id" to exactly match original behavior.

Miscellaneous

  • Doctests are now written in Python 3.
  • make test now validates MANIFEST.in using check-manifest. (#461)
  • Many new alpha diversity equations added to skbio.diversity.alpha documentation. (#321)
  • Order of lowercase and validate keywords swapped in DNA, RNA, and Protein.

Version 0.4.0 (2015-07-08)

Initial beta release. In addition to the changes detailed below, the following subpackages have been mostly or entirely rewritten and most of their APIs are substantially different (and improved!):

  • skbio.sequence
  • skbio.io

The APIs of these subpackages are now stable, and all others are experimental. See the API stability docs for more details, including what we mean by stable and experimental in this context. We recognize that this is a lot of backward-incompatible changes. To avoid these types of changes being a surprise to our users, our public APIs are now decorated to make it clear to developers when an API can be relied upon (stable) and when it may be subject to change (experimental).

Features

  • Added skbio.stats.composition for analyzing data made up of proportions
  • Added new skbio.stats.evolve subpackage for evolutionary statistics. Currently contains a single function, hommola_cospeciation, which implements a permutation-based test of correlation between two distance matrices.
  • Added support for skbio.io.util.open_file and skbio.io.util.open_files to pull files from HTTP and HTTPS URLs. This behavior propagates to the I/O registry.
  • FASTA/QUAL (skbio.io.format.fasta) and FASTQ (skbio.io.format.fastq) readers now allow blank or whitespace-only lines at the beginning of the file, between records, or at the end of the file. A blank or whitespace-only line in any other location will continue to raise an error #781.
  • scikit-bio now ignores leading and trailing whitespace characters on each line while reading FASTA/QUAL and FASTQ files.
  • Added ratio parameter to skbio.stats.power.subsample_power. This allows the user to calculate power on groups for uneven size (For example, draw twice as many samples from Group B than Group A). If ratio is not set, group sizes will remain equal across all groups.
  • Power calculations (skbio.stats.power.subsample_power and skbio.stats.power.subsample_paired_power) can use test functions that return multiple p values, like some multivariate linear regression models. Previously, the power calculations required the test to return a single p value.
  • Added skbio.util.assert_data_frame_almost_equal function for comparing pd.DataFrame objects in unit tests.

Performance enhancements

  • The speed of quality score decoding has been significantly improved (~2x) when reading fastq files.
  • The speed of NucleotideSequence.reverse_complement has been improved (~6x).

Bug fixes

  • Changed Sequence.distance to raise an error any time two sequences are passed of different lengths regardless of the distance_fn being passed. (#514)
  • Fixed issue with TreeNode.extend where if given the children of another TreeNode object (tree.children), both trees would be left in an incorrect and unpredictable state. (#889)
  • Changed the way power was calculated in subsample_paired_power to move the subsample selection before the test is performed. This increases the number of Monte Carlo simulations performed during power estimation, and improves the accuracy of the returned estimate. Previous power estimates from subsample_paired_power should be disregarded and re-calculated. (#910)
  • Fixed issue where randdm was attempting to create asymmetric distance matrices.This was causing an error to be raised by the DistanceMatrix constructor inside of the randdm function, so that randdm would fail when attempting to create large distance matrices. (#943)

Deprecated functionality

  • Deprecated skbio.util.flatten. This function will be removed in scikit-bio 0.3.1. Please use standard python library functionality described here Making a flat list out of lists of lists, Flattening a shallow list (#833)
  • Deprecated skbio.stats.power.bootstrap_power_curve will be removed in scikit-bio 0.4.1. It is deprecated in favor of using subsample_power or sample_paired_power to calculate a power matrix, and then the use of confidence_bounds to calculate the average and confidence intervals.

Backward-incompatible changes

  • Removed the following deprecated functionality:
    • skbio.parse subpackage, including SequenceIterator, FastaIterator, FastqIterator, load, parse_fasta, parse_fastq, parse_qual, write_clustal, parse_clustal, and FastqParseError; please use skbio.io instead.
    • skbio.format subpackage, including fasta_from_sequence, fasta_from_alignment, and format_fastq_record; please use skbio.io instead.
    • skbio.alignment.SequenceCollection.int_map; please use SequenceCollection.update_ids instead.
    • skbio.alignment.SequenceCollection methods to_fasta and toFasta; please use SequenceCollection.write instead.
    • constructor parameter in skbio.alignment.Alignment.majority_consensus; please convert returned biological sequence object manually as desired (e.g., str(seq)).
    • skbio.alignment.Alignment.to_phylip; please use Alignment.write instead.
    • skbio.sequence.BiologicalSequence.to_fasta; please use BiologicalSequence.write instead.
    • skbio.tree.TreeNode methods from_newick, from_file, and to_newick; please use TreeNode.read and TreeNode.write instead.
    • skbio.stats.distance.DissimilarityMatrix methods from_file and to_file; please use DissimilarityMatrix.read and DissimilarityMatrix.write instead.
    • skbio.stats.ordination.OrdinationResults methods from_file and to_file; please use OrdinationResults.read and OrdinationResults.write instead.
    • skbio.stats.p_value_to_str; there is no replacement.
    • skbio.stats.subsample; please use skbio.stats.subsample_counts instead.
    • skbio.stats.distance.ANOSIM; please use skbio.stats.distance.anosim instead.
    • skbio.stats.distance.PERMANOVA; please use skbio.stats.distance.permanova instead.
    • skbio.stats.distance.CategoricalStatsResults; there is no replacement, please use skbio.stats.distance.anosim or skbio.stats.distance.permanova, which will return a pandas.Series object.
  • skbio.alignment.Alignment.majority_consensus now returns BiologicalSequence('') if the alignment is empty. Previously, '' was returned.
  • min_observations was removed from skbio.stats.power.subsample_power and skbio.stats.power.subsample_paired_power. The minimum number of samples for subsampling depends on the data set and statistical tests. Having a default parameter to set unnecessary limitations on the technique.

Miscellaneous

  • Changed testing procedures
    • Developers should now use make test
    • Users can use python -m skbio.test
    • Added skbio.util._testing.TestRunner (available through skbio.util.TestRunner). Used to provide a test method for each module init file. This class represents a unified testing path which wraps all skbio testing functionality.
    • Autodetect Python version and disable doctests for Python 3.
  • numpy is no longer required to be installed before installing scikit-bio!
  • Upgraded checklist.py to check source files non-conforming to new header style. (#855)
  • Updated to use natsort >= 4.0.0.
  • The method of subsampling was changed for skbio.stats.power.subsample_paired_power. Rather than drawing a paired sample for the run and then subsampling for each count, the subsample is now drawn for each sample and each run. In test data, this did not significantly alter the power results.
  • checklist.py now enforces __future__ imports in .py files.

Version 0.2.3 (2015-02-13)

Features

  • Modified skbio.stats.distance.pwmantel to accept a list of filepaths. This is useful as it allows for a smaller amount of memory consumption as it only loads two matrices at a time as opposed to requiring that all distance matrices are loaded into memory.
  • Added skbio.util.find_duplicates for finding duplicate elements in an iterable.

Bug fixes

  • Fixed floating point precision bugs in Alignment.position_frequencies, Alignment.position_entropies, Alignment.omit_gap_positions, Alignment.omit_gap_sequences, BiologicalSequence.k_word_frequencies, and SequenceCollection.k_word_frequencies (#801).

Backward-incompatible changes

  • Removed feature_types attribute from BiologicalSequence and all subclasses (#797).
  • Removed find_features method from BiologicalSequence and ProteinSequence (#797).
  • BiologicalSequence.k_word_frequencies now returns a collections.defaultdict of type float instead of type int. This only affects the "default" case, when a key isn't present in the dictionary. Previous behavior would return 0 as an int, while the new behavior is to return 0.0 as a float. This change also affects the defaultdicts that are returned by SequenceCollection.k_word_frequencies.

Miscellaneous

  • DissimilarityMatrix and DistanceMatrix now report duplicate IDs in the DissimilarityMatrixError message that can be raised during validation.

Version 0.2.2 (2014-12-04)

Features

  • Added plot method to skbio.stats.distance.DissimilarityMatrix for creating basic heatmaps of a dissimilarity/distance matrix (see #684). Also added _repr_png_ and _repr_svg_ methods for automatic display in the IPython Notebook, with png and svg properties for direct access.
  • Added __str__ method to skbio.stats.ordination.OrdinationResults.
  • Added skbio.stats.distance.anosim and skbio.stats.distance.permanova functions, which replace the skbio.stats.distance.ANOSIM and skbio.stats.distance.PERMANOVA classes. These new functions provide simpler procedural interfaces to running these statistical methods. They also provide more convenient access to results by returning a pandas.Series instead of a CategoricalStatsResults object. These functions have more extensive documentation than their previous versions. If significance tests are suppressed, p-values are returned as np.nan instead of None for consistency with other statistical methods in scikit-bio. #754
  • Added skbio.stats.power for performing empirical power analysis. The module uses existing datasets and iteratively draws samples to estimate the number of samples needed to see a significant difference for a given critical value.
  • Added skbio.stats.isubsample for subsampling from an unknown number of values. This method supports subsampling from multiple partitions and does not require that all items be stored in memory, requiring approximately O(N*M)`` space where Nis the number of partitions andM` is the maximum subsample size.
  • Added skbio.stats.subsample_counts, which replaces skbio.stats.subsample. See deprecation section below for more details (#770).

Bug fixes

  • Fixed issue where SSW wouldn't compile on i686 architectures (#409).

Deprecated functionality

  • Deprecated skbio.stats.p_value_to_str. This function will be removed in scikit-bio 0.3.0. Permutation-based p-values in scikit-bio are calculated as (num_extreme + 1) / (num_permutations + 1), so it is impossible to obtain a p-value of zero. This function historically existed for correcting the number of digits displayed when obtaining a p-value of zero. Since this is no longer possible, this functionality will be removed.
  • Deprecated skbio.stats.distance.ANOSIM and skbio.stats.distance.PERMANOVA in favor of skbio.stats.distance.anosim and skbio.stats.distance.permanova, respectively.
  • Deprecated skbio.stats.distance.CategoricalStatsResults in favor of using pandas.Series to store statistical method results. anosim and permanova return pandas.Series instead of CategoricalStatsResults.
  • Deprecated skbio.stats.subsample in favor of skbio.stats.subsample_counts, which provides an identical interface; only the function name has changed. skbio.stats.subsample will be removed in scikit-bio 0.3.0.

Backward-incompatible changes

  • Deprecation warnings are now raised using DeprecationWarning instead of UserWarning (#774).

Miscellaneous

  • The pandas.DataFrame returned by skbio.stats.distance.pwmantel now stores p-values as floats and does not convert them to strings with a specific number of digits. p-values that were previously stored as "N/A" are now stored as np.nan for consistency with other statistical methods in scikit-bio. See note in "Deprecated functionality" above regarding p_value_to_str for details.
  • scikit-bio now supports versions of IPython < 2.0.0 (#767).

Version 0.2.1 (2014-10-27)

This is an alpha release of scikit-bio. At this stage, major backwards-incompatible API changes can and will happen. Unified I/O with the scikit-bio I/O registry was the focus of this release.

Features

  • Added strict and lookup optional parameters to skbio.stats.distance.mantel for handling reordering and matching of IDs when provided DistanceMatrix instances as input (these parameters were previously only available in skbio.stats.distance.pwmantel).
  • skbio.stats.distance.pwmantel now accepts an iterable of array_like objects. Previously, only DistanceMatrix instances were allowed.
  • Added plot method to skbio.stats.ordination.OrdinationResults for creating basic 3-D matplotlib scatterplots of ordination results, optionally colored by metadata in a pandas.DataFrame (see #518). Also added _repr_png_ and _repr_svg_ methods for automatic display in the IPython Notebook, with png and svg properties for direct access.
  • Added skbio.stats.ordination.assert_ordination_results_equal for comparing OrdinationResults objects for equality in unit tests.
  • BiologicalSequence (and its subclasses) now optionally store Phred quality scores. A biological sequence's quality scores are stored as a 1-D numpy.ndarray of nonnegative integers that is the same length as the biological sequence. Quality scores can be provided upon object instantiation via the keyword argument quality, and can be retrieved via the BiologicalSequence.quality property. BiologicalSequence.has_quality is also provided for determining whether a biological sequence has quality scores or not. See #616 for more details.
  • Added BiologicalSequence.sequence property for retrieving the underlying string representing the sequence characters. This was previously (and still is) accessible via BiologicalSequence.__str__. It is provided via a property for convenience and explicitness.
  • Added BiologicalSequence.equals for full control over equality testing of biological sequences. By default, biological sequences must have the same type, underlying sequence of characters, identifier, description, and quality scores to compare equal. These properties can be ignored via the keyword argument ignore. The behavior of BiologicalSequence.__eq__/__ne__ remains unchanged (only type and underlying sequence of characters are compared).
  • Added BiologicalSequence.copy for creating a copy of a biological sequence, optionally with one or more attributes updated.
  • BiologicalSequence.__getitem__ now supports specifying a sequence of indices to take from the biological sequence.
  • Methods to read and write taxonomies are now available under skbio.tree.TreeNode.from_taxonomy and skbio.tree.TreeNode.to_taxonomy respectively.
  • Added SequenceCollection.update_ids, which provides a flexible way of updating sequence IDs on a SequenceCollection or Alignment (note that a new object is returned, since instances of these classes are immutable). Deprecated SequenceCollection.int_map in favor of this new method; it will be removed in scikit-bio 0.3.0.
  • Added skbio.util.cardinal_to_ordinal for converting a cardinal number to ordinal string (e.g., useful for error messages).
  • New I/O Registry: supports multiple file formats, automatic file format detection when reading, unified procedural skbio.io.read and skbio.io.write in addition to OOP interfaces (read/write methods) on the below objects. See skbio.io for more details.
    • Added "clustal" format support:
      • Has sniffer
      • Readers: Alignment
      • Writers: Alignment
    • Added "lsmat" format support:
      • Has sniffer
      • Readers: DissimilarityMatrix, DistanceMatrix
      • Writers: DissimilarityMatrix, DistanceMatrix
    • Added "ordination" format support:
      • Has sniffer
      • Readers: OrdinationResults
      • Writers: OrdinationResults
    • Added "newick" format support:
      • Has sniffer
      • Readers: TreeNode
      • Writers: TreeNode
    • Added "phylip" format support:
      • No sniffer
      • Readers: None
      • Writers: Alignment
    • Added "qseq" format support:
      • Has sniffer
      • Readers: generator of BiologicalSequence or its subclasses, SequenceCollection, BiologicalSequence, NucleotideSequence, DNASequence, RNASequence, ProteinSequence
      • Writers: None
    • Added "fasta"/QUAL format support:
      • Has sniffer
      • Readers: generator of BiologicalSequence or its subclasses, SequenceCollection, Alignment, BiologicalSequence, NucleotideSequence, DNASequence, RNASequence, ProteinSequence
      • Writers: same as readers
    • Added "fastq" format support:
      • Has sniffer
      • Readers: generator of BiologicalSequence or its subclasses, SequenceCollection, Alignment, BiologicalSequence, NucleotideSequence, DNASequence, RNASequence, ProteinSequence
      • Writers: same as readers

Bug fixes

  • Removed constructor parameter from Alignment.k_word_frequencies, BiologicalSequence.k_words, BiologicalSequence.k_word_counts, and BiologicalSequence.k_word_frequencies as it had no effect (it was never hooked up in the underlying code). BiologicalSequence.k_words now returns a generator of BiologicalSequence objects instead of strings.
  • Modified the Alignment constructor to verify that all sequences have the same length, if not, raise an AlignmentError exception. Updated the method Alignment.subalignment to calculate the indices only once now that identical sequence length is guaranteed.

Deprecated functionality

  • Deprecated constructor parameter in Alignment.majority_consensus in favor of having users call str on the returned BiologicalSequence. This parameter will be removed in scikit-bio 0.3.0.

  • Existing I/O functionality deprecated in favor of I/O registry, old functionality will be removed in scikit-bio 0.3.0. All functionality can be found at skbio.io.read, skbio.io.write, and the methods listed below:

    • Deprecated the following "clustal" readers/writers:

      • write_clustal -> Alignment.write
      • parse_clustal -> Alignment.read

    • Deprecated the following distance matrix format ("lsmat") readers/writers:

      • DissimilarityMatrix.from_file -> DissimilarityMatrix.read
      • DissimilarityMatrix.to_file -> DissimilarityMatrix.write
      • DistanceMatrix.from_file -> DistanceMatrix.read
      • DistanceMatrix.to_file -> DistanceMatrix.write

    • Deprecated the following ordination format ("ordination") readers/writers:

      • OrdinationResults.from_file -> OrdinationResults.read
      • OrdinationResults.to_file -> OrdinationResults.write

    • Deprecated the following "newick" readers/writers:

      • TreeNode.from_file -> TreeNode.read
      • TreeNode.from_newick -> TreeNode.read
      • TreeNode.to_newick -> TreeNode.write

    • Deprecated the following "phylip" writers:

      • Alignment.to_phylip -> Alignment.write

    • Deprecated the following "fasta"/QUAL readers/writers:

      • SequenceCollection.from_fasta_records -> SequenceCollection.read
      • SequenceCollection.to_fasta -> SequenceCollection.write
      • fasta_from_sequences -> skbio.io.write(obj, into=<file>, format='fasta')
      • fasta_from_alignment -> Alignment.write
      • parse_fasta -> skbio.io.read(<fasta>, format='fasta')
      • parse_qual -> skbio.io.read(<fasta>, format='fasta', qual=<file>)
      • BiologicalSequence.to_fasta -> BiologicalSequence.write

    • Deprecated the following "fastq" readers/writers:

      • parse_fastq -> skbio.io.read(<fastq>, format='fastq')
      • format_fastq_record -> skbio.io.write(<fastq>, format='fastq')

Backward-incompatible changes

  • skbio.stats.distance.mantel now returns a 3-element tuple containing correlation coefficient, p-value, and the number of matching rows/cols in the distance matrices (n). The return value was previously a 2-element tuple containing only the correlation coefficient and p-value.
  • skbio.stats.distance.mantel reorders input DistanceMatrix instances based on matching IDs (see optional parameters strict and lookup for controlling this behavior). In the past, DistanceMatrix instances were treated the same as array_like input and no reordering took place, regardless of ID (mis)matches. array_like input behavior remains the same.
  • If mismatched types are provided to skbio.stats.distance.mantel (e.g., a DistanceMatrix and array_like), a TypeError will be raised.

Miscellaneous

  • Added git timestamp checking to checklist.py, ensuring that when changes are made to Cython (.pyx) files, their corresponding generated C files are also updated.
  • Fixed performance bug when instantiating BiologicalSequence objects. The previous runtime scaled linearly with sequence length; it is now constant time when the sequence is already a string. See #623 for details.
  • IPython and six are now required dependencies.

Version 0.2.0 (2014-08-07)

This is an initial alpha release of scikit-bio. At this stage, major backwards-incompatible API changes can and will happen. Many backwards-incompatible API changes were made since the previous release.

Features

  • Added ability to compute distances between sequences in a SequenceCollection object (#509), and expanded Alignment.distance to allow the user to pass a function for computing distances (the default distance metric is still scipy.spatial.distance.hamming) (#194).
  • Added functionality to not penalize terminal gaps in global alignment. This functionality results in more biologically relevant global alignments (see #537 for discussion of the issue) and is now the default behavior for global alignment.
  • The python global aligners (global_pairwise_align, global_pairwise_align_nucleotide, and global_pairwise_align_protein) now support aligning pairs of sequences, pairs of alignments, and a sequence and an alignment (see #550). This functionality supports progressive multiple sequence alignment, among other things such as adding a sequence to an existing alignment.
  • Added StockholmAlignment.to_file for writing Stockholm-formatted files.
  • Added strict=True optional parameter to DissimilarityMatrix.filter.
  • Added TreeNode.find_all for finding all tree nodes that match a given name.

Bug fixes

  • Fixed bug that resulted in a ValueError from local_align_pairwise_nucleotide (see #504) under many circumstances. This would not generate incorrect results, but would cause the code to fail.

Backward-incompatible changes

  • Removed skbio.math, leaving stats and diversity to become top level packages. For example, instead of from skbio.math.stats.ordination import PCoA you would now import from skbio.stats.ordination import PCoA.
  • The module skbio.math.gradient as well as the contents of skbio.math.subsample and skbio.math.stats.misc are now found in skbio.stats. As an example, to import subsample: from skbio.stats import subsample; to import everything from gradient: from skbio.stats.gradient import *.
  • The contents of skbio.math.stats.ordination.utils are now in skbio.stats.ordination.
  • Removed skbio.app subpackage (i.e., the application controller framework) as this code has been ported to the standalone burrito Python package. This code was not specific to bioinformatics and is useful for wrapping command-line applications in general.
  • Removed skbio.core, leaving alignment, genetic_code, sequence, tree, and workflow to become top level packages. For example, instead of from skbio.core.sequence import DNA you would now import from skbio.sequence import DNA.
  • Removed skbio.util.exception and skbio.util.warning (see #577 for the reasoning behind this change). The exceptions/warnings were moved to the following locations:
  • FileFormatError, RecordError, FieldError, and EfficiencyWarning have been moved to skbio.util
  • BiologicalSequenceError has been moved to skbio.sequence
  • SequenceCollectionError and StockholmParseError have been moved to skbio.alignment
  • DissimilarityMatrixError, DistanceMatrixError, DissimilarityMatrixFormatError, and MissingIDError have been moved to skbio.stats.distance
  • TreeError, NoLengthError, DuplicateNodeError, MissingNodeError, and NoParentError have been moved to skbio.tree
  • FastqParseError has been moved to skbio.parse.sequences
  • GeneticCodeError, GeneticCodeInitError, and InvalidCodonError have been moved to skbio.genetic_code
  • The contents of skbio.genetic_code formerly skbio.core.genetic_code are now in skbio.sequence. The GeneticCodes dictionary is now a function genetic_code. The functionality is the same, except that because this is now a function rather than a dict, retrieving a genetic code is done using a function call rather than a lookup (so, for example, GeneticCodes[2] becomes genetic_code(2).
  • Many submodules have been made private with the intention of simplifying imports for users. See #562 for discussion of this change. The following list contains the previous module name and where imports from that module should now come from.
  • skbio.alignment.ssw to skbio.alignment
  • skbio.alignment.alignment to skbio.alignment
  • skbio.alignment.pairwise to skbio.alignment
  • skbio.diversity.alpha.base to skbio.diversity.alpha
  • skbio.diversity.alpha.gini to skbio.diversity.alpha
  • skbio.diversity.alpha.lladser to skbio.diversity.alpha
  • skbio.diversity.beta.base to skbio.diversity.beta
  • skbio.draw.distributions to skbio.draw
  • skbio.stats.distance.anosim to skbio.stats.distance
  • skbio.stats.distance.base to skbio.stats.distance
  • skbio.stats.distance.permanova to skbio.stats.distance
  • skbio.distance to skbio.stats.distance
  • skbio.stats.ordination.base to skbio.stats.ordination
  • skbio.stats.ordination.canonical_correspondence_analysis to skbio.stats.ordination
  • skbio.stats.ordination.correspondence_analysis to skbio.stats.ordination
  • skbio.stats.ordination.principal_coordinate_analysis to skbio.stats.ordination
  • skbio.stats.ordination.redundancy_analysis to skbio.stats.ordination
  • skbio.tree.tree to skbio.tree
  • skbio.tree.trie to skbio.tree
  • skbio.util.misc to skbio.util
  • skbio.util.testing to skbio.util
  • skbio.util.exception to skbio.util
  • skbio.util.warning to skbio.util
  • Moved skbio.distance contents into skbio.stats.distance.

Miscellaneous

  • Relaxed requirement in BiologicalSequence.distance that sequences being compared are of equal length. This is relevant for Hamming distance, so the check is still performed in that case, but other distance metrics may not have that requirement. See #504).
  • Renamed powertrip.py repo-checking script to checklist.py for clarity.
  • checklist.py now ensures that all unit tests import from a minimally deep API. For example, it will produce an error if skbio.core.distance.DistanceMatrix is used over skbio.DistanceMatrix.
  • Extra dimension is no longer calculated in skbio.stats.spatial.procrustes.
  • Expanded documentation in various subpackages.
  • Added new scikit-bio logo. Thanks Alina Prassas!

Version 0.1.4 (2014-06-25)

This is a pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.

Features

  • Added Python implementations of Smith-Waterman and Needleman-Wunsch alignment as skbio.core.alignment.pairwise.local_pairwise_align and skbio.core.alignment.pairwise.global_pairwise_align. These are much slower than native C implementations (e.g., skbio.core.alignment.local_pairwise_align_ssw) and as a result raise an EfficencyWarning when called, but are included as they serve as useful educational examples as they’re simple to experiment with.
  • Added skbio.core.diversity.beta.pw_distances and skbio.core.diversity.beta.pw_distances_from_table. These provide convenient access to the scipy.spatial.distance.pdist beta diversity metrics from within scikit-bio. The skbio.core.diversity.beta.pw_distances_from_table function will only be available temporarily, until the biom.table.Table object is merged into scikit-bio (see #489), at which point skbio.core.diversity.beta.pw_distances will be updated to use that.
  • Added skbio.core.alignment.StockholmAlignment, which provides support for parsing Stockholm-formatted alignment files and working with those alignments in the context RNA secondary structural information.
  • Added skbio.core.tree.majority_rule function for computing consensus trees from a list of trees.

Backward-incompatible changes

  • Function skbio.core.alignment.align_striped_smith_waterman renamed to local_pairwise_align_ssw and now returns an Alignment object instead of an AlignmentStructure
  • The following keyword-arguments for StripedSmithWaterman and local_pairwise_align_ssw have been renamed:
    • gap_open -> gap_open_penalty
    • gap_extend -> gap_extend_penalty
    • match -> match_score
    • mismatch -> mismatch_score
  • Removed skbio.util.sort module in favor of natsort package.

Miscellaneous

  • Added powertrip.py script to perform basic sanity-checking of the repo based on recurring issues that weren't being caught until release time; added to Travis build.
  • Added RELEASE.md with release instructions.
  • Added intersphinx mappings to docs so that "See Also" references to numpy, scipy, matplotlib, and pandas are hyperlinks.
  • The following classes are no longer namedtuple subclasses (see #359 for the rationale):
    • skbio.math.stats.ordination.OrdinationResults
    • skbio.math.gradient.GroupResults
    • skbio.math.gradient.CategoryResults
    • skbio.math.gradient.GradientANOVAResults
  • Added coding guidelines draft.
  • Added new alpha diversity formulas to the skbio.math.diversity.alpha documentation.

Version 0.1.3 (2014-06-12)

This is a pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.

Features

  • Added enforce_qual_range parameter to parse_fastq (on by default, maintaining backward compatibility). This allows disabling of the quality score range-checking.
  • Added skbio.core.tree.nj, which applies neighbor-joining for phylogenetic reconstruction.
  • Added bioenv, mantel, and pwmantel distance-based statistics to skbio.math.stats.distance subpackage.
  • Added skbio.math.stats.misc module for miscellaneous stats utility functions.
  • IDs are now optional when constructing a DissimilarityMatrix or DistanceMatrix (monotonically-increasing integers cast as strings are automatically used).
  • Added DistanceMatrix.permute method for randomly permuting rows and columns of a distance matrix.
  • Added the following methods to DissimilarityMatrix: filter, index, and __contains__ for ID-based filtering, index lookup, and membership testing, respectively.
  • Added ignore_comment parameter to parse_fasta (off by default, maintaining backward compatibility). This handles stripping the comment field from the header line (i.e., all characters beginning with the first space) before returning the label.
  • Added imports of BiologicalSequence, NucleotideSequence, DNA, DNASequence, RNA, RNASequence, Protein, ProteinSequence, DistanceMatrix, align_striped_smith_waterman, SequenceCollection, Alignment, TreeNode, nj, parse_fasta, parse_fastq, parse_qual, FastaIterator, FastqIterator, SequenceIterator in skbio/__init__.py for convenient importing. For example, it's now possible to from skbio import Alignment, rather than from skbio.core.alignment import Alignment.

Bug fixes

  • Fixed a couple of unit tests that could fail stochastically.
  • Added missing __init__.py files to a couple of test directories so that these tests won't be skipped.
  • parse_fastq now raises an error on dangling records.
  • Fixed several warnings that were raised while running the test suite with Python 3.4.

Backward-incompatible changes

  • Functionality imported from skbio.core.ssw must now be imported from skbio.core.alignment instead.

Miscellaneous

  • Code is now flake8-compliant; added flake8 checking to Travis build.
  • Various additions and improvements to documentation (API, installation instructions, developer instructions, etc.).
  • __future__ imports are now standardized across the codebase.
  • New website front page and styling changes throughout. Moved docs site to its own versioned subdirectories.
  • Reorganized alignment data structures and algorithms (e.g., SSW code, Alignment class, etc.) into an skbio.core.alignment subpackage.

Version 0.1.1 (2014-05-16)

Fixes to setup.py. This is a pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.

Version 0.1.0 (2014-05-15)

Initial pre-alpha release. At this stage, major backwards-incompatible API changes can and will happen.