Pyteomics

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- 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`.

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- 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.

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- 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`.

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- 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.htmlgeneral-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.

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- 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).

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