path: root/CHANGELOG

3.1
---

This release offers integration with the great :py:mod:`pandas` library.
Working with :py:func:`qvalues` and :py:func:`!filter` functions
is now much easier if you have your PSMs in a :py:class:`DataFrame`.
Many search engines use CSV as their output format, allowing direct
creation of :py:class:`DataFrame` objects. New functions
:py:func:`pyteomics.tandem.DataFrame` and :py:func:`pyteomics.pepxml.DataFrame`
faciliatate creation of DataFrames from corresponding formats.

Also, :py:func:`qvalues`, :py:func:`!filter` and :py:func:`fdr` functions can now use
posterior error probabilities (PEPs) instead of using decoys for q-value calculation.

 - In :py:func:`qvalues` and :py:func:`!filter` functions,
   `key` and `is_decoy` can now be array-like objects or strings
   (as well as functions and iterators).
   If a string is given, it is used as a field name in the PSM array
   or :py:class:`DataFrame`. :py:func:`fdr` functions also support strings
   and iterables as arguments.

 - New parameter `pep` in :py:func:`qvalues`, :py:func:`!filter` and :py:func:`fdr` functions.
   It can be callable, array-like, or iterator. Conflicts with decoy-related
   parameters. Compatible with `key`, but makes it optional.

 - Fixed the behavior of :py:func:`filter.chain` functions. They now treat
   the `full_output` argument the same way as :py:func:`!filter` functions.

 - Fixed the issue that caused exceptions when calling :py:func:`fasta.decoy_db`
   and :py:func:`fasta.write_decoy_db` with explicitly given `mode` (signature
   for creation of :py:class:`pyteomics.auxiliary.FileReader` objects slightly changed).

 - Pyteomics now uses `setuptools` and is a namespace package.

 - Minor fixes.


API changes
...........

- Default value of `remove_decoy` in :py:func:`qvalues` is now :py:const:`False`.

3.0.1
-----

 - Added `legend_kwargs` as a keyword argument to
   :py:func:`pyteomics.pylab_aux.scatter_trend`.

 - Minor fixes.

3.0.0
-----

 - XML parsers are now implemented as objects, each format has its own class.
   Those classes can be instantiated using the same arguments as :py:func:`read`
   functions accepted, and support direct iteration and the ``with`` syntax.
   The :py:func:`read` functions are now simple aliases to the corresponding
   constructors.

 - As a result, functions :py:func:`iterfind`, :py:func:`version_info` and
   :py:func:`get_by_id` functions are now deprecated in favor of methods
   :py:meth:`iterfind` and :py:meth:`get_by_id` and attribute
   :py:attr:`version_info` of corresponding instances.

 - In :py:func:`pyteomics.mgf.write`, the order of keys and the format of values
   are now controlled via module-level variables.

 - In :py:mod:`pyteomics.electrochem`, correction for pK of terminal groups
   depending on the terminal residue is implemented; example set of pK and
   corrected pK added.

 - Imports of external dependencies are delayed where possible, so that
   unnecessary :py:exc:`ImportErrors` do not occur.

 - :py:func:`local_fdr` renamed to :py:func:`qvalues` in :py:mod:`pepxml`,
   :py:mod:`mzid`, :py:mod:`tandem` and :py:mod:`auxiliary`.
   :py:func:`local_fdr` did not reflect the semantics of the function.
   The algorithm has been also corrected so that the array of q-values
   is always sorted (as it should be by definition).

 - :py:func:`qvalues` now also accepts a parameter `full_output` which keeps the
   PSMs alongside their scores and associated q-values.

 - All :py:func:`fdr`, :py:func:`qvalues`, and :py:func:`!filter` functions
   now accept a new parameter `correction`. It is used for more accurate
   estimation of the number of false positives using TDA (paper with explanation
   submitted to JPR).

 - :py:func:`!filter` functions now support both iterator protocol and context
   manager protocol. They now also accept the `full_output` parameter, which has
   the following meaning: if :py:const:`True` (default), then an array of PSMs
   is directly returned by the function. Otherwise, an iterator is returned, as
   before. The array takes some memory, but this way is usually around 2x faster.

 - New function :py:func:`pyteomics.pylab_aux.plot_qvalue_curve`.

 - :py:class:`pyteomics.mass.Composition` objects now have a :py:meth:`mass`
   method (equivalent to :py:func:`pyteomics.mass.calculate_mass`.

 - Also, :py:class:`Composition` and objects returned by
   :py:func:`pyteomics.parser.amino_acid_composition` now inherit from
   :py:class:`collections.defaultdict` **and** :py:class:`collections.Counter`.

 - Decoy-related functions in :py:mod:`pyteomics.fasta` now accept a new parameter
   `keep_nterm` that preserves the N-terminal residue in the generated decoy
   sequences.

 - Minor fixes.

API changes
...........

 - In :py:func:`pyteomics.pylab_aux.scatter_trend`, keyword arguments for
   :py:func:`pylab.scatter` and :py:func:`pylab.plot` are now accepted as dicts
   `scatter_kwargs` and `plot_kwargs`. Keyword argument `alpha` is now not
   accepted and should be put in the appropriate dict.
 - In :py:func:`pyteomics.pylab_aux.plot_function_3d` and
   :py:func:`pyteomics.pylab_aux.plot_function_contour`, arbitrary kwargs can
   now also be passed to the plotting function.
 - :py:func:`!filter` functions do not support context manager protocol by
   default. To keep using them as iterators / context managers, specify
   ``full_output=False`` (see above for details).

2.5.5
-----

Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects
:py:func:`pyteomics.mzid.read` with ``retrieve_refs=True``.

2.5.4
-----

 - New functions :py:func:`local_fdr` in :py:mod:`pepxml`, :py:mod:`mzid`, and
   :py:mod:`tandem`. The function returns a NumPy array with PSM scores and
   corresponding values of local FDR.

 - New parameter `iterative` in :py:func:`read` functions of XML parsing
   modules. Parsing of mzIdentML files with ``retrieve_refs=True`` got
   significantly faster.

2.5.3
-----

 - Universally applicable modifications are now allowed in
   :py:func:`pyteomics.parser.isoforms`.
 - It is now also possible to specify non-terminal modifications which are
   only applicable to terminal residues.
 - Fix in :py:func:`pyteomics.parser.parse`: if the `labels` argument is
   provided, it needs to contain standard terminal groups if they are present
   in the sequence or if `show_unmodified_termini` is set to :py:const:`True`.
 - :py:class:`pyteomics.mass.Composition` instances are now pickleable.
 - Performance improvements.

2.5.2
-----

 - New parameter `reverse` in all :py:func:`!filter` functions.
 - New function :py:func:`pyteomics.mass.fast_mass2`, which is analogous to
   :py:func:`pyteomicsmass.fast_mass`, but supports full *modX* notation and
   is several times slower.
 - Fix in :py:func:`pyteomics.pepxml.read` for compatibility with files
   produced with Mascot2XML utility.
 - Unknown labels now allowed in :py:mod:`pyteomics.electrochem` and
   :py:mod:`pyteomics.achrom` functions in accordance with new general policy.

2.5.1
-----

 - Bugfixes in :py:func:`pyteomics.parser.isoforms`:
  - handling of the `labels` argument is now in accordance with new policy
  - solved memory problems when using `max_mods`
 - :py:func:`pyteomics.parser.cleave` does not require a valid *modX* sequence
   by default.

2.5.0
-----

 - :py:func:`pyteomics.parser.amino_acid_composition` now accepts "split"
   parsed sequences.

 - Cleavage rules in :py:data:`pyteomics.parser.expasy_rules` updated.

 - Helper function :py:func:`pyteomics.parser.num_sites` counts the number
   of cleavage sites in a sequence.

 - Helper function :py:func:`pyteomics.parser.match_modX` does essentially
   the same as :py:func:`pyteomics.parser.is_modX`, but returns a
   :py:class:`re.match` object or :py:const:`None` instead of a :py:class:`bool`.

 - Bugfix in :py:func:`pyteomics.auxiliary.filter`, which didn't work correctly
   with iterators.

 - Added a new parameter ``max_mods`` in :py:func:`pyteomics.parser.isoforms`.

API changes
...........

 - The boolean ``overlap`` parameter in :py:func:`pyteomics.parser.cleave` is
   replaced with an integer ``min_length``. Since ``min_length`` uses
   :py:func:`pyteomics.parser.length`, the ``labels`` keyword argument is now
   accepted by :py:func:`cleave` and :py:func:`num_sites`, if needed. With
   carefully designed cleavage rules, all cleavage functions work
   with *modX* sequences.

 - The ``labels`` argument in :py:func:`pyteomics.parser.parse` and related
   functions has changed its meaning. :py:func:`parse` won't raise an exception
   for non-standard labels in sequences if the ``labels`` keyword argument is
   not given.

 - The *modX* notation specification is now more strict to avoid ambiguity:
   only zero or two terminal groups can be present in a *modX* sequence.
   Sequences with one terminal group specified will be supported where possible,
   but be advised that sequences such as "H-OH" are intrinsically ambiguous.

2.4.3
-----

 - Added the ``ratio`` keyword argument for FDR calculation.

 - Minor changes in :py:func:`iterfind` functions of file parsers.

 - Bugfix in :py:func:`pyteomics.mgf.write` (duplication of pepmass key).

 - Removed non-functional parameter ``read_schema`` for
   :py:func:`pyteomics.tandem.read`.

2.4.2
-----

 - Bugfix in :py:func:`pyteomics.mass.most_probable_isotopic_composition`.
   The bug manifested itself after version **2.4.0**, when
   :py:data:`pyteomics.mass.nist_mass` was expanded. Also, the format of the
   returned value is now in accordance with the documentation.

2.4.1
-----

 - New function :py:func:`pyteomics.auxiliary.filter` for filtering lists
   of PSMs not coming directly from files in supported formats.

 - Also, a format-agnostic helper function :py:func:`pyteomics.auxiliary.fdr`.

2.4.0
-----

 - New functions for filtering to a certain FDR level based on target-decoy
   strategy, as well as for FDR estimation, in :py:mod:`pyteomics.tandem`,
   :py:mod:`pyteomics.pepxml` and :py:mod:`pyteomics.mzid`. The functions are
   called :py:func:`!filter` (beware of shadowing the built-in function) and
   :py:func:`fdr` (in each of the modules). Chained versions
   :py:func:`filter.chain` and :py:func:`filter.chain.from_iterable` are
   also available. See `Data Access <data.html#general-notes>`_ for more info.

 - New function :py:func:`pyteomics.parser.coverage` for sequence coverage
   calculation.

 - New function :py:func:`pyteomics.fasta.decoy_chain`, a chained version of
   :py:func:`pyteomics.fasta.decoy_db`.

 - New elements in :py:data:`pyteomics.mass.nist_mass`. Pretty much all elements
   are there now.

 - Fix in :py:func:`pyteomics.parser.parse` to cover some fancy corner cases.

 - Bugfix in :py:mod:`pyteomics.tandem`: modification info is now fully extracted.

 - :py:func:`pyteomics.mass.isotopic_composition_abundance` is now able to
   calculate abundances for larger molecules.

   .. note::
       Rounding errors may be significant in this case.

2.3.0
-----

 - New parameter "read_schema" in :py:func:`read` functions of XML parsing modules.
   When set to :py:const:`False`, disables the attempts to fetch an auxiliary file
   and obtain structure information about the file being parsed.

 - New function :py:func:`chain` in all modules that have a :py:func:`read`
   function, for convenient chaining of multiple files. :py:func:`chain` only
   works as a context manager. Use :py:func:`itertools.chain` in other cases.
   The ``chain.from_iterable`` form is also available as a context manager.

 - New function :py:func:`pyteomics.auxiliary.print_tree` for exploration of
   complex nested dicts produced by XML parsers.

 - New sets of retention coefficients in :py:mod:`pyteomics.achrom`.

 - Bugfix in :py:mod:`pyteomics.pepxml`. The bug caused an exception when parsing
   some pepXML files.

 - The output of :py:func:`pyteomics.mgf.read` now always contains a masked
   array of charges.

 - Other minor fixes.

API change
..........

 - In :py:func:`pyteomics.mgf.read` the precursor charge is now always represented
   by a list of ints (a :py:class:`ChargeList` object).

2.2.2
-----

 - Bugfix in :py:mod:`pyteomics.tandem`. The info about all proteins is now
   extracted.

2.2.1
-----

 - Update parsers for FASTA headers.

 - NamedTuple for FASTA entries is now defined globally, which should solve
   pickling problems.

2.2.0
-----

 - New module :py:mod:`pyteomics.tandem` for reading output files of X!Tandem
   search engine.

2.1.6
-----

 - Fix in :py:mod:`pyteomics.pepxml`. pepXML files generated by TPP are now
   processed without errors.


2.1.5
-----

 - Fix in :py:mod:`pyteomics.pepxml`. 'modified_peptide' is now always available.

 - Fix in :py:mod:`pyteomics.mass` (issue #2 in the bug tracker).

 - Improved arithmetics for :py:class:`Composition` objects.

2.1.4
-----

 - In :py:mod:`fasta`, :py:func:`decoy_db` now doesn't write to file, but returns
   an iterator over FASTA records. The old :py:func:`decoy_db` is now called
   :py:func:`write_decoy_db`, which is equivalent to :py:func:`decoy_db` combined
   with :py:func:`write`.

Bugfixes:

 - In :py:func:`pyteomics.mgf.read`, the charges, if present, are returned as a
   masked array now. Previously, an exception occurred if charges were missing
   for some of the fragments.

 - Values in :py:data:`mass.nist_mass` corrected.

 - Other minor corrections.

2.1.3
-----

 - Adjust the behavior affected by the bug fixed in 2.1.2. `name` attributes
   of `<cvParam>` elements in the absence of `value` attributes are now collected
   in a list under the `'name'` key.

 - Add support for overlapping matches in :py:func:`parser.cleave`.

2.1.2
-----

 - Bugfix in XML parsers. The bug caused the mzML parser break on some files.
   The fix can slightly change the format of the output.

2.1.1
-----

 - Rename keys in the dicts returned by :py:func:`mgf.read` to facilitate
   writing code working with both MGF and mzML.

 - The items yielded by :py:func:`fasta.read` now have attributes `description`
   and `sequence`.

2.1.0
-----

 - New sets of retention coefficients in :py:mod:`achrom`.

 - :py:class:`mass.Composition` now only stores non-zero ints.

 - :py:mod:`fasta` now has tools for parsing of FASTA headers.

 - File parsers now implement the `context manager protocol
   <http://docs.python.org/reference/datamodel.html#with-statement-context-managers>`_.
   We recommend using `with` statements to avoid resource leaks.

API changes
...........

 - 'pepmass' is now a tuple in the output of :py:func:`mgf.read` (to allow
   reading precursor intensities).

 - new function :py:func:`fasta.parse` for convenient parsing of FASTA headers.

 - :py:data:`fasta.std_parsers` stores parsers for common UniProt header formats.

 - new parameter *parser* in :py:func:`fasta.read` allows to apply parsing while
   reading a FASTA file.

 - `close` parameter removed in all functions that do file I/O. The unified
   behavior is: if the parameter is a file object, it won't be closed by the
   function. If a file path is given, the file object will be created and closed
   inside the corresponding function.

2.0.3
-----

 - Added new class :py:class:`pyteomics.mass.Unimod`. The interface is
   experimental and may change.

 - Improved :py:func:`iterfind` function in XML-reading modules.

 - :py:class:`pyteomics.mass.Composition` objects now support multiplication by
   :py:class:`int`.

 - Bugfix in :py:func:`auxiliary.linear_regression`.

2.0.2
-----

 - Added new function :py:func:`iterfind` in :py:mod:`pyteomics.mzid`,
   :py:mod:`pyteomics.pepxml` and :py:mod:`pyteomics.mzml`.

2.0.1
-----

API changes
...........

 - :py:func:`pyteomics.parser.peptide_length` is renamed to
   :py:func:`pyteomics.parser.length`.

2.0.0
-----

 - Added :py:mod:`mzid` module for parsing of mzIdentML files.

 - Fixed bugs, improved tests.

API changes
...........

 - top-module functions in :py:mod:`fasta`, :py:mod:`mgf`, :py:mod:`mzml`,
   :py:mod:`pepxml`, as well as :py:mod:`mzid`, are now called :py:func:`read`.

 - in :py:mod:`parser`, :py:func:`parse_sequence` renamed to :py:func:`parse`.
   It now accepts an optional parameter `allow_unknown_modifications`.

 - :py:func:`mgf.write_mgf` and :py:func:`fasta.write_fasta` renamed to
   :py:func:`write`.

 - the output format of all :py:func:`read` functions has changed.

1.2.5
-----

 - Include Apache license version 2.0:
   http://www.opensource.org/licenses/Apache-2.0

 - Minor bugfix in :py:mod:`pyteomics.fasta`.

1.2.4
-----

 - Changes in :py:mod:`pyteomics.mass`.

API changes
...........

 - :py:class:`Composition` objects can be created using positional first
   argument, which will be treated as a sequence or (upon failure) as a formula.
   This means that all functions relying on Composition
   (:py:func:`calculate_mass`, :py:func:`most_probable_isotopic_composition`,
   :py:func:`isotopic_composition_abundance`) allow that as well. However, it's
   of no use for the latter.

 - :py:class:`Composition` entries for modifications can be added to *aa_comp*
   and used in composition and mass calculations. This way the specified group
   will be added to any residue bearing this modification.

 - That being said, the :py:func:`add_modifications` function is not needed
   anymore and has been removed.

 - Addition and subtraction of :py:class:`Composition` objects now produces a
   :py:class:`Composition` object, allowing addition/subtraction of multiple
   objects.

 - :py:class:`Composition` is now a subclass of
   :py:class:`collections.defaultdict` so one can safely retrieve values
   without checking if a key exists.

1.2.3
-----

 - :py:func:`pyteomics.parser.isoforms` now allows terminal modifications.

 - Bugfixes in :py:func:`pyteomics.parser.parse_sequence`.

 - New function :py:func:`pyteomics.parser.tostring` converts parsed sequences
   to strings.

 - Helper function :py:func:`pyteomics.parser.is_modX` added to check *modX* labels.

API changes
...........

 - :py:func:`pyteomics.parser.isoforms` now returns a generator object

1.2.2
-----

 - Bugfix in :py:mod:`pyteomics.pepxml`: modification info is now extracted.
 - New optional bool argument 'split' in :py:func:`pyteomics.parser.parse_sequence()`
   allows to generate a list of tuples where modifications are separated from the
   residues instead of a regular list of labels. In *labels* not only *modX* labels
   are now allowed, but also separate *mod* prefixes. Such modifications are
   assumed to be applicable to any residue.


1.2.1
-----

 - Memory usage **significantly** decreased when parsing large mzML and pepXML
   files.

1.2.0
-----

 - Added support for Python 3. Python 2.7 is still supported, Python 2.6 is not.

1.1.1
-----

 - New function called :py:func:`add_modifications()` added in
   :py:mod:`pyteomics.mass`. It updates *aa_comp*.
 - Also, :py:func:`pyteomics.parser.isoforms` is a new function to get
   all possible modified sequences of a peptide.

1.1.0
-----

 - New module added - :py:mod:`pyteomics.mgf`. It is intended for reading and
   writing files in Mascot Generic Format.

1.0.2
-----

 - In :py:mod:`pyteomics.pepxml` module, now all search hits are read from file
   (not only the top hit).

API changes:
............

 - :py:func:`pyteomics.pepxml.read`: information specific to search hits is now
   stored in a list under the ``'search_hits'`` key. The list is sorted by hit
   rank.


1.0.1
-----

 - Fix compatibility issues in :py:mod:`pyteomics.pepxml` module.

1.0.0
-----

 - The first public release of Pyteomics.

API changes:
............

 - :py:mod:`pyteomics.achrom`: rename ``'length correction factor'`` to
   ``'length correction parameter'``.

   - :py:func:`pyteomics.achrom.get_RCs_vary_lcf` was renamed to
     :py:func:`pyteomics.achrom.get_RCs_vary_lcp`.
   - `length_correction_factor` keyword argument of
     :py:func:`pyteomics.achrom.get_RCs` was renamed to `lcp`.