Pyteomics

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Technical release to update the package metadata on PyPI.
Project documentation on pythonhosted.org has been deleted.
Latest documentation is available at: https://pyteomics.readthedocs.io/.

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- Preserve accession information on cvParam elements in mzML parser.
Dictionaries produced by the parser can now be queried by accession using
:py:func:`pyteomics.auxiliary.cvquery`.
*(Contributed by J. Klein)*

- Add optional `decode_binary` argument in
:py:class:`pyteomics.mzml.MzML` and :py:class:`pyteomics.mzxml.MzXML`.
When set to `False`, the parsers provide binary records suitable for decoding on demand.
*(Contributed by J. Klein)*

- Add method :py:meth:`write_byte_offsets` in :py:class:`pyteomics.mzml.MzML`,
:py:class:`pyteomics.mzxml.MzXML` and :py:class:`pyteomics.mzid.MzIdentML`.
Byte offsets can be loaded later to speed up random access.
*(Contributed by J. Klein)*

- Random access to MGF spectrum entries.

- Add function :py:func:`pyteomics.mgf.get_spectrum`.

- Add class :py:class:`pyteomics.mgf.MGF`. :py:func:`mgf.read` is now an alias to the class.
The class can be used for indexing using spectrum titles.

This functionality will be changed in upcoming versions.

- New module :py:mod:`pyteomics.protxml` for parsing of ProteinProphet output files.

- Add PeptideProphet and iProphet analysis information to the output of :py:func:`pyteomics.pepxml.DataFrame`.

- New parameter `huge_tree` in XML parser constructors and :py:func:`read` functions.
It is passed to the underlying :py:mod:`lxml` calls. Default value is `False`.
Set to `True` to overcome errors such as: `XMLSyntaxError: xmlSAX2Characters: huge text node`.

- New parameter `skip_empty_cvparam_values` in XML parser constructors.
It instructs the parser to treat the empty "value" attributes in cvParam elements as if they were not there.
This is helpful in cases when such empty "values" are present in one vendor's file and absent in another:
enabling the parameter will result in more unified output.
Default value is `False`.

- Change the default value for `read_schema` to :py:const:`False` in XML parsing modules.

- Change the default value for `retrieve_refs` to :py:const:`True` in MzIdentML constructor.

- Implement `retrieve_refs` for :py:class:`pyteomics.mzml.MzML`.
*(Contributed by J. Klein)*

- New parameter `keep_cterm` in decoy generation functions in :py:mod:`pyteomics.fasta`.

- New parameters `decoy_prefix` and `decoy_suffix` in all format-specific FDR filtering functions.
If the standard :py:func:`is_decoy` function works for your files, you can use these parameters to
specify either the prefix or the suffix appended to the protein names in decoy entries.

- New ion types in :py:data:`pyteomics.mass.std_ion_comp`.

- Bugfixes.

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- New module :py:mod:`pyteomics.ms1` for parsing of MS1 files.

- :py:class:`mass.Composition` constructor now accepts `ion_type` and `charge` parameters.

- New functions :py:func:`pyteomics.mzid.DataFrame` and :py:func:`pyteomics.mzid.filter_df`.
Their behavior may be refined later on.

- Changes in behavior of :py:func:`pyteomics.auxiliary.filter` and :py:func:`pyteomics.auxiliary.qvalues`:

- both functions now always return DataFrames with :py:class:`pandas.DataFrame` input and `full_output=True`.

- string values of `key`, `is_decoy` and `pep` are substituted with simple itemgetter functions for
non-pandas, non-numpy input;

- additional parameters `score_label`, `decoy_label`, `pep_label`, and `q_label` for output control.

- Performance optimizations in XML parsing code.

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- Add selenocysteine ("U") and pyrrolysine ("O") to :py:data:`pyteomics.mass.std_aa_mass` and
:py:data:`pyteomics.mass.std_aa_comp`.

- An optional parameter `encoding` is now accepted by text file readers (:py:func:`pyteomics.mgf.read`
and :py:func:`pyteomics.fasta.read`). This can be useful for MGF files with non-ASCII spectrum
titles or comments.

- New function :py:func:`pyteomics.mass.mass.isotopologues`.

- Performance improvements in :py:func:`pyteomics.electrochem.pI`.

- Fix the issue in :py:mod:`pyteomics.xml` which resulted in very long processing times for indexed XML files
with a byte ordering mark (BOM).

- Support all standard and non-standard data array names in :py:mod:`pyteomics.mzml`.

- Change default value of ``retrieve_refs`` in :py:func:`pyteomics.mzid.read` to :py:const:`True`.

- Preserve unit information extracted from cvParam tags in PSI XML files.

- Fix in :py:mod:`pyteomics.mzxml`, other minor fixes.

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- New module :py:mod:`pyteomics.mzxml` for parsing of MzXML files.

- New parameter `dtype` in :py:func:`pyteomics.mgf.read`, :py:func:`pyteomics.mzml.read`
and :py:func:`pyteomics.mzxml.read`
allows changing the dtype of arrays yielded by the parsers.

- :py:mod:`pyteomics.featurexml` moved into a subpackage :py:mod:`pyteomics.openms`.

- New module :py:mod:`pyteomics.openms.trafoxml` for OpenMS transformation files.

- Bugfix in XML indexing code to make it work on Python 3.x versions prior to 3.5.

- Bugfix in :py:func:`pyteomics.pylab_aux.scatter_trend` (support for lists and other non-ndarrays).

- Performance improvements in :py:mod:`pyteomics.achrom` calibration functions.

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New submodule :py:mod:`pyteomics.featurexml` with a parser for OpenMS **featureXML** files.