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CHANGELOG
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4.6.4b3
-------
- Make :py:class:`proforma.MassModification` objects hashable
(`#130 <https://github.com/levitsky/pyteomics/pull/130>`_ by Joshua Klein).
- Fix `#132 <https://github.com/levitsky/pyteomics/issues/132>`_
(`#133 <https://github.com/levitsky/pyteomics/pull/133>`_ by Joshua Klein).
- Fix thermolysin cleavage rule (`#135 <https://github.com/levitsky/pyteomics/issues/135>`_).
- Fix `#136 <https://github.com/levitsky/pyteomics/issues/136>`_.
- :py:func:`pyteomics.mass.mass.calculate_mass` now supports `ProForma <https://www.psidev.info/proforma>`_.
A sequence or a :py:class:`proforma.ProForma` object can be passed with the `proforma` keyword argument
(`#137 <https://github.com/levitsky/pyteomics/pull/137>`_).
4.6.3
-----
- Fix `#122 <https://github.com/levitsky/pyteomics/issues/122>`_.
- Fix `#124 <https://github.com/levitsky/pyteomics/issues/124>`_
(in `#125 <https://github.com/levitsky/pyteomics/pull/125>`_ by Seth Just).
- Fix `#128 <https://github.com/levitsky/pyteomics/issues/128>`_
(in `#129 <https://github.com/levitsky/pyteomics/pull/129>`_ by Joshua Klein).
4.6.2
-----
- :py:func:`pyteomics.fasta.write` can now write entries with parsed sequences
(`#120 <https://github.com/levitsky/pyteomics/pull/120>`_ by Vladimir Gorshkov, Joshua Klein and Lev Levitsky).
- Fix `#119 <https://github.com/levitsky/pyteomics/issues/119>`_.
- Fix import issue with :py:mod:`pyteomics.pylab_aux`.
4.6.1
-----
- Make :py:func:`pyteomics.mgf.write` work with a regular list of ints as "charge" param.
- Add mean absolute error (MAE) regression in :py:mod:`pyteomics.achrom`
(`#117 <https://github.com/levitsky/pyteomics/pull/117>`_ by Mark Ivanov).
- Fix `#115 <https://github.com/levitsky/pyteomics/issues/115>`_ and `#118 <https://github.com/levitsky/pyteomics/issues/118>`_.
- Remove :py:class:`auxiliary.Version`. :py:class:`pyteomics.version.VersionInfo` can be used instead.
- For target-decoy calculations, :py:mod:`pandas` is assumed to be 0.17 or newer.
4.6
---
- When passing an existing file (by name) to :py:func:`pyteomics.mgf.write` or :py:func:`pyteomics.fasta.write` and
other writing functions, **the file will be opened for writing by default**. Previously, it would be opened for
appending with a warning about the upcoming change. Please be aware that existing files will be overwritten
if passed by name. The rationale for this is better reproducibility if the same code is run multiple
times. You can use the `file_mode` argument of the writing functions to override this behaviour, or pass your own
file objects.
- Add a special warning when trying to write a single spectrum with :py:func:`pyteomics.mgf.write`.
See also: `Writing one or more MGF spectra to a file <https://github.com/levitsky/pyteomics/discussions/109>`_.
- In :py:func:`pyteomics.mass.mass.calculate_mass`, the `absolute` parameter is now `True` by default.
When calculating *m/z* for negative charges, the returned value will be positive by default.
- Fix issue #98 (`#99 <https://github.com/levitsky/pyteomics/pull/99>`_ and
`#101 <https://github.com/levitsky/pyteomics/pull/101>`_ by Joshua Klein).
- Fix issue #91 (`#92 <https://github.com/levitsky/pyteomics/pull/92>`_ by Joshua Klein).
- Fix issue #96.
- Update the UniProt header pattern (fix rare parsing errors with
:py:class:`pyteomics.fasta.UniProt` and :py:class:`pyteomics.fasta.IndexedUniProt`) in
`#93 <https://github.com/levitsky/pyteomics/pull/93>`_.
- Update the UniRef header pattern (fix parsing errors with
:py:class:`pyteomics.fasta.UniRef` and :py:class:`pyteomics.fasta.IndexedUniRef`) in
`#102 <https://github.com/levitsky/pyteomics/pull/102>`_. Some keys are removed from the output.
- Fix pickling issues with :py:class:`pyteomics.mgf.IndexedMGF`, :py:class:`pyteomics.ms1.IndexedMS1`,
:py:class:`pyteomics.ms2.IndexedMS2` (#108).
- Add "charge array" and "resolution array" to the output of MS2 parsers (#108). Add new arguments `read_charges`
and `read_resolutions` to disable parsing, and `convert_arrays` to govern the creation of NumPy arrays
(and masked arrays).
4.5.6
-----
- New function :py:func:`pyteomics.proforma.set_unimod_path` allowing the ProForma parsing machinery
to work with a local Unimod copy (`#85 <https://github.com/levitsky/pyteomics/pull/85>`_ by Joshua Klein).
See `documentation <https://pyteomics.readthedocs.io/en/latest/api/proforma.html#cv-disk-caching>`_ for a usage example.
- New method :py:meth:`pyteomics.proforma.Proforma.fragments` to generate m/z for an ion series
(`#85 <https://github.com/levitsky/pyteomics/pull/85>`_ by Joshua Klein).
- New function :py:func:`pyteomics.parser.to_proforma` helps convert *modX* sequences to ProForma.
- Fix: prevent :func:`pyteomics.mass.mass.fast_mass2` from changing `aa_mass`.
- Update :py:func:`pyteomics.pylab_aux.annotate_spectrum` for compatibility with latest :py:mod:`spectrum_utils`.
Pyteomics is now compatible with :py:mod:`spectrum_utils` 0.4.0 and newer.
4.5.5
-----
- Fix issue #77.
4.5.4
-----
- Fix issue #74.
- In :func:`pyteomics.auxiliary.fdr`, raise :exc:`PyteomicsError` instead of :exc:`ZeroDivisionError` when
using formula 1 on input without any target PSMs.
- Provide more accurate amino acid masses in :py:data:`mass.std_aa_mass`.
- Fix SyntaxError in :py:mod:`pyteomics.pylab_aux` on Python 2.7.
4.5.3
-----
- Fix ThreadPool shutdown and add new parameter `ephemeral_pool` in :py:class:`pyteomics.usi.PROXIAggregator`
(`#67 <https://github.com/levitsky/pyteomics/pull/67>`_ by Joshua Klein).
- Bugfix in `pyteomics.proforma.GenericModificationResolver` (`#68 <https://github.com/levitsky/pyteomics/issues/68>`_ by Joshua Klein).
- New helper function :py:func:`pyteomics.fasta.decoy_entries`.
- New arguments `charge_carrier`, `absolute` in :py:func:`mass.calculate_mass` and
:py:meth:`mass.Composition.mass` (`#61 <https://github.com/levitsky/pyteomics/pull/61>`_).
Charge is now only handled in :py:meth:`Composition.mass` and not :py:meth:`Composition.__init__`.
- Bugfix in :py:mod:`pyteomics.tandem` (`#71 <https://github.com/levitsky/pyteomics/pull/71>`_ by @superrino130).
4.5.2
-----
- Support Python 3.10.
4.5.1
-----
- Add `max_length` parameter in :py:func:`pyteomics.parser.cleave`.
- Bugfix in :py:func:`pyteomics.parser.cleave` for `semi=True`.
- Add `regex` parameter in :py:func:`pyteomics.parser.cleave` and warn for possible typos in cleavage rule names.
- Add functions :py:func:`parser.icleave` (generator) and :py:func:`parser.xcleave` (list) to produce
peptide sequences with indices and possible repetitions.
- Bugfixes (`#63 <https://github.com/levitsky/pyteomics/pull/63>`_ and `#64 <https://github.com/levitsky/pyteomics/pull/64>`_
by Joshua Klein).
4.5
---
- Add support for `mzMLb <https://www.biorxiv.org/content/10.1101/2020.02.13.947218v3>`_
(`#35 <https://github.com/levitsky/pyteomics/pull/35>`_
and `#38 <https://github.com/levitsky/pyteomics/pull/38>`_ by Joshua Klein)
with new module :py:mod:`pyteomics.mzmlb`.
- Add ProteomeExchange backend for PROXI requests and implement an aggregator for responses from all backends
(`#36 <https://github.com/levitsky/pyteomics/pull/36>`_,
`#45 <https://github.com/levitsky/pyteomics/pull/45>`_, and
`#55 <https://github.com/levitsky/pyteomics/pull/55>`_ by Joshua Klein)
in :py:mod:`pyteomics.usi`.
- Add support for `ProForma <https://www.psidev.info/proforma>`_
(`#37 <https://github.com/levitsky/pyteomics/pull/37>`_ by Joshua Klein)
in new module :py:mod:`pyteomics.proforma`.
- New arguments `keep_nterm_M` and `fix_aa` in :py:func:`pyteomics.fasta.shuffle`
(`#54 <https://github.com/levitsky/pyteomics/pull/54>`_ by Vladimir Gorshkov).
- Fix for unwanted warnings in :py:func:`pyteomics.auxiliary.file_helpers._check_use_index` when
`use_index` is explicitly passed (`#52 <https://github.com/levitsky/pyteomics/issues/52>`_).
- Update the default XML schema for featureXML and fix issues with incorrectly specified data types
(`#53 <https://github.com/levitsky/pyteomics/pull/53>`_).
- Add a new backend for spectrum annotation and plotting. :py:func:`pyteomics.pylab_aux.plot_spectrum` and
:py:func:`pyteomics.pylab_aux.annotate_spectrum` can now use
`spectrum_utils <https://github.com/bittremieux/spectrum_utils>`_ under the hood
(`#43 <https://github.com/levitsky/pyteomics/pull/43>`_).
See new `Example 4 <examples/example_annotation.html>`_ for demonstration.
- New function :py:func:`pyteomics.pylab_aux.mirror` for making a
`spectrum_utils <https://github.com/bittremieux/spectrum_utils>`_ mirror plot.
- :py:func:`pyteomics.pylab_aux.plot_spectrum` and :py:func:`pyteomics.pylab_aux.annotate_spectrum` now
always return :py:class:`matplotlib.pyplot.Axes`.
- Add a warning when passing an existing file by name in writing functions.
The default mode for output files will change from `'a'` to `'w'` in a future version.
4.4.2
-----
- Add cleavage rules from `MS ontology <http://purl.obolibrary.org/obo/MS_1001045>`_ as
:py:data:`pyteomics.parser.psims_rules`. :py:func:`pyteomics.parser.cleave` now understands keys and accessions from
:py:data:`psims_rules` as rules.
- Improve mzIdentML parser performance (and possibly others in some cases) by relying more on offset indexes
(`#34 <https://github.com/levitsky/pyteomics/pull/34>`_ by Joshua Klein).
- Extend the :py:class:`pyteomics.mztab.MzTab` parser with auto-generated properties. Almost all metadata entities are
now exposed as properties on the parser object (`#23 <https://github.com/levitsky/pyteomics/pull/23>`_ by Joshua Klein).
- Fix the version parsing in :py:mod:`pyteomics.mztab` to support shorter vMzTab version strings
(`#24 <https://github.com/levitsky/pyteomics/pull/24>`_ by Donavan See).
- Tweak the :py:class:`pyteomics.pepxml.PepXML` parser to present some values that were previously reported as None.
- Fix compatibility with :py:mod:`SQLAlchemy` 1.4 (`#32 <https://github.com/levitsky/pyteomics/pull/32>`_ by Joshua Klein).
4.4.1
-----
- Further tweaked behavior of :py:func:`pyteomics.auxiliary.file_helpers._check_use_index`, which is responsible for
handling of `use_index` in :py:func:`read` functions in parser modules.
- Fix indexing when element identifiers contain XML-escaped characters
(`#20 <https://github.com/levitsky/pyteomics/pull/20>`_ by Joshua Klein).
- Add support for MzTab 2.0 (`#22 <https://github.com/levitsky/pyteomics/pull/22>`_ by @annalefarova).
- Also, check out the `Pyteomics Discussions page <https://github.com/levitsky/pyteomics/discussions>`_!
You can use it to share your thoughts, ask questions, discuss coding practices, etc.
4.4
---
- New module :py:mod:`pyteomics.usi` implements a minimal Universal Spectrum Identifier parser and PROXI client
(`#11 <https://github.com/levitsky/pyteomics/pull/11>`_ by Joshua Klein).
- Support peak annotations in MGF (`#12 <https://github.com/levitsky/pyteomics/pull/12>`_ by Julian Müller).
- Provide version information in :py:mod:`pyteomics.version` (`#14 <https://github.com/levitsky/pyteomics/pull/14>`_).
- Make the order of isoforms reproducible in :py:func:`pyteomics.parser.isoforms`
(`#15 <https://github.com/levitsky/pyteomics/issues/15>`_).
- Rename `types` keyword argument to `ion_types` in :py:func:`pyteomics.pylab_aux.annotate_spectrum`.
- Fix `#16 <https://github.com/levitsky/pyteomics/issues/16>`_, a bug introduced in 4.3.3.
4.3.3
-----
- Add :py:func:`pyteomics.electrochem.gravy` (`#9 <https://github.com/levitsky/pyteomics/pull/9>`_ by Vladimir Gorshkov).
- Fixes and improvements in :py:func:`pyteomics.pepxml.roc_curve` (`#10 <https://github.com/levitsky/pyteomics/pull/10>`_
by Andrey Rozenberg).
- Changes in guessing behavior of :py:func:`read` functions.
In modules that implement :ref:`indexing parsers <indexing>` for non-XML formats (MGF, FASTA, PEFF, ms1/ms2),
when a parser is instantiated using :py:func:`read`, the parser class to instantiate is guessed
based on the mode of the file object passed to :py:func:`read` (text or binary).
With some file-like objects, mode cannot be easily deduced without consuming some of the data.
You will now see more warnings in case `use_index` is not explicitly passed to :py:func:`read` and reading mode is not obvious.
There will also be warnings if `use_index` is specified but the file is opened in the wrong mode.
To avoid all of this, you are encouraged to instantiate parser classes directly,
or explicitly specify `use_index` to :py:func:`read` in all corner cases.
4.3.2
-----
Fix `#7 <https://github.com/levitsky/pyteomics/issues/7>`_.
4.3.1
-----
Technical release.
4.3
---
First release after the move to Github. Issue and PR numbers from now on refer to the
`Github repo <https://github.com/levitsky/pyteomics>`_. Archive of the Bibucket issues and PRs is stored
`here <https://levitsky.github.io/bitbucket_backup/#!/levitsky/pyteomics>`_.
Changes in this release:
- New module :py:mod:`pyteomics.openms.idxml`.
- Fix `#3 <https://github.com/levitsky/pyteomics/issues/3>`_, `#5 <https://github.com/levitsky/pyteomics/issues/5>`_,
and some issues in :py:mod:`tandem`.
4.2
---
- Changes in XML XPath implementation.
For standard XML parser classes, this only means a minor change in performance
(should be a slight improvement, most noticeable for :py:class:`TandemXML`).
- For custom classes: the implementation of xpath evaluation in :py:meth:`pyteomics.xml.XML.iterfind` has changed.
Pseudo-conditions are now not supported. Instead, an attempt is made to support full XPath.
The main difference is that the XPath is evaluated on XML elements,
whereas pseudo-conditions used to be evaluated for complete Python dictionaries.
To reproduce old behavior, you can just write an explicit `if` statement at an appropriate place.
New implementation allows actually skipping the elements that do not satisfy the XPath predicate.
When writing classes which by default iterate over elements based on a complex XPath, set
:py:attr:`_default_iter_path` instead of :py:attr:`_default_iter_tag`.
.. warning ::
Beware that if :py:attr:`_default_iter_path` differs from :py:attr:`_default_iter_tag` and you use indexing,
all elements corresponding to :py:attr:`_default_iter_tag` will be indexed.
This is a limitation of the index building procedure.
This discrepancy will lead to confusing behavior
(length checks, membership tests and other things based on index
will not correspond to items returned by iteration).
:py:meth:`map` calls will also operate on the full index.
- New keyword arguments `queue_size`, `queue_timeout` and `processes` for indexed parsers with support for :py:meth:`map`.
- New method :py:meth:`mass.Unimod.by_id`.
Also, :py:class:`mass.Unimod` now supports dict-like queries with record IDs.
- Reduce memory footprint for unit primitives (PR #35 by Joshua Klein).
- New functions :py:func:`pyteomics.auxiliary.sigma_T` and :py:func:`pyteomics.auxiliary.sigma_fdr`.
- Fix issues #44, #46, #47, #48.
4.1.2
-----
Bugfix: fix the standard mass value for pyrrolysine (issue #42).
4.1.1
-----
- Add `numpress <https://dx.doi.org/10.1074%2Fmcp.O114.037879>`_ support for mzML and mzXML files.
To read files compressed with Numpress, install `pynumpress`
(`PyPI <https://pypi.org/project/pynumpress/>`_, `GitHub <https://github.com/mobiusklein/pynumpress>`_).
- Bugfixes.
API changes
...........
- In :py:func:`ms1.read` and :py:func:`ms2.read`, the default value for `use_index` is now :py:const:`False`.
Using the indexed parsers may result in incorrect behavior if the "first" scan number in S-lines is not unique.
4.1
---
- New module :py:mod:`pyteomics.mztab` provides a parser for `mzTab files <http://www.psidev.info/mztab>`_.
- New module :py:mod:`pyteomics.ms2` provides a parser for **ms2** files.
This is in fact an alias to :py:mod:`ms1`, which handles both formats.
- Added index saving functionality for :py:class:`pyteomics.mgf.IndexedMGF`.
- New helper functions :py:func:`pyteomics.pylab_aux.plot_spectrum` and :py:func:`pyteomics.pylab_aux.annotate_spectrum`.
- The `rule` and `exception` arguments in :py:func:`pyteomics.parser.cleave` can be keys from :py:const:`expasy_rules`.
- Fixes.
4.0.1
-----
Fix issue `#35 <hhttps://levitsky.github.io/bitbucket_backup/#!/levitsky/pyteomics/issues/35/page/1>`_
(incorrect order of deserialized offset indexes on older Python versions).
4.0
---
.. seealso::
`Pyteomics 4.0: five years of development of a Python proteomics framework
<https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00717>`_
- Add parameters `semi` and `exception` in :py:func:`pyteomics.parser.cleave`.
- Add new parameter `encoding` in file writers.
- Add new parameters `write_charges` and `use_numpy` in :py:func:`pyteomics.mgf.write`.
Speed up the writing when :py:mod:`numpy` is available.
- :ref:`Indexing text parsers <indexing>`. This release introduces a family of parser classes for text files.
These parsers create byte offsets of indexed entries to allow random access by unique key or by positional index,
"rich" access by slices and, in case of MGF/mzML/mzXML, by retention time range.
All indexing parsers, text- or XML-based, now have a unified interface.
- New class :py:class:`pyteomics.mgf.IndexedMGF` is now the recommended way to parse MGF files.
It supports fast access by spectrum titles by using an index of byte offsets.
The old, sequential parser is preserved under its name, :py:class:`pyteomics.mgf.MGF`.
The function :py:func:`pyteomics.mgf.read` now returns an instance of one of the two classes,
based on the `use_index` argument and the type of `source`.
The common ancestor class, :py:class:`pyteomics.mgf.MGFBase`, can be used for type checking.
- New FASTA parsing classes:
- :py:class:`pyteomics.fasta.FASTABase` - common ancestor, suitable for type checking;
- :py:class:`pyteomics.fasta.FASTA` - text-mode, sequential parser; does
what the old :py:func:`fasta.read` was doing. Additionally, the following subclasses perform
format-specific parsing of FASTA headers:
- :py:class:`pyteomics.fasta.UniProt`;
- :py:class:`pyteomics.fasta.UniParc`;
- :py:class:`pyteomics.fasta.UniRef`;
- :py:class:`pyteomics.fasta.UniMes`;
- :py:class:`pyteomics.fasta.SPD`;
- :py:class:`pyteomics.fasta.NCBI`;
- :py:class:`pyteomics.fasta.IndexedFASTA` - binary-mode, indexing parser.
Supports direct indexing by header string;
- :py:class:`pyteomics.fasta.TwoLayerIndexedFASTA` - additionally supports
indexing by extracted header fields. Format-specific second indexes are available in
subclasses:
- :py:class:`pyteomics.fasta.IndexedUniProt`;
- :py:class:`pyteomics.fasta.IndexedUniParc`;
- :py:class:`pyteomics.fasta.IndexedUniRef`;
- :py:class:`pyteomics.fasta.IndexedUniMes`;
- :py:class:`pyteomics.fasta.IndexedSPD`;
- :py:class:`pyteomics.fasta.IndexedNCBI`.
:py:func:`pyteomics.fasta.read` now returns an instance of one of these classes,
depending on the arguments `use_index` and `flavor`.
- :py:class:`pyteomics.ms1.IndexedMS1` and :py:class:`pyteomics.ms1.MS1` are available for ms1 format.
*(In collaboration with J. Klein)*
- Multiprocessing support: all indexed XML and text file parsers now expose a :py:meth:`map` method.
This method can map a user-supplied function to each file entry in separate processes (or simply
parallelize the parsing itself).
Additionally, objects returned by :py:func:`chain` functions and :py:meth:`iterfind` methods also expose
the :py:meth:`map` interface to allow parallelizing the work over multiple files and when iterating over
non-default XML tree elements.
The order of entries is not preserved in the output.
*(In collaboration with J. Klein)*
- New module :py:mod:`pyteomics.peff` implements the :py:class:`IndexedPEFF` parser for protein databases
in the new PSI standard format, `PEFF <http://www.psidev.info/peff>`_. *(Contributed by J. Klein)*
- New module :py:mod:`pyteomics.traml` implements the :py:class:`TraML` parser for the PSI standard format
for SRM data, `TraML <http://www.psidev.info/traml>`_. *(In collaboration with J. Klein)*
- :py:class:`pyteomics.protxml.ProtXML` now also supports indexing and multiprocessing.
- Removed parameter `skip_empty_cvparam_values` in XML parsers. In cvParam elements, missing "value"
attribute is now always equivalent to the case when it is equal to an empty string. This affects
the structure of items produced by MzML and MzIdentML parsers.
- Multiple fixes and improvements.
3.5.1
-----
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/.
3.5
---
- 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.
3.4.2
-----
- 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.
3.4.1
-----
- 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.
3.4
---
- 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.
3.3.1
-----
New submodule :py:mod:`pyteomics.featurexml` with a parser for OpenMS **featureXML** files.
3.3
---
- mzML and mzIdentML parsers can now create an index of element offsets.
This allows quick random access to elements by unique ID.
- mzML parsers now come in two flavors: :py:class:`pyteomics.mzml.MzML` and
:py:class:`pyteomics.mzml.PreIndexedMzML`. The latter uses the byte offsets
listed at the end of the file.
- New parameters `convert_arrays` and `read_charges` in :py:func:`mgf.read`
allow using it without :py:mod:`numpy` and possibly improve performance.
The default behavior is retained.
- Performance optimizations in :py:func:`mgf.read` and :py:func:`parser.cleave`.
- New decoy generation mode called "fused decoy", described in the `paper accepted to JASMS
<http://dx.doi.org/10.1007/s13361-016-1436-7>`_.
API changes
...........
- :py:func:`pyteomics.parser.cleave` no longer accepts the `labels` argument.
It is emphasized that the input sequences are expected to be in plain one-letter
notation, but no checks are performed.
- :py:func:`DataFrame` functions in :py:mod:`pepxml` and :py:mod:`tandem` now
extract more protein-related information. The list-like protein-related values
can be reported as lists or packed into strings, depending on the optional
paramter `sep`. Some column names have changed as a result.
- Call signatures of :py:func:`pyteomics.fasta.decoy_sequence` and the functions using it
are slightly changed. Standard modes are now also exposed as individual functions.
3.2
---
New submodule :py:mod:`pyteomics.mass.unimod` contains rewritten machinery
for handling of Unimod relational databases (contributed by Joshua Klein).
This is a substitution and extension for the old :py:class:`mass.Unimod` class.
:py:mod:`pyteomics.mass.unimod` requires SQLAlchemy.
Other changes:
- New function :py:func:`pyteomics.auxiliary.linear_regression_perpendicular`
provides a linear fit minimizing distances from data points to the fit line
(as opposed to :py:func:`pyteomics.auxiliary.linear_regression`, which
minimizes vertical distances).
- Both new and old linear regression functions now accept a single array of shape (N, 2).
- :py:func:`pyteomics.pylab_aux.scatter_trend` now has an optional parameter
`regression` which can be a callable performing the regression.
Also, the regression equation is now the label of the regression line, not
the scatter plot.
- Another two new parameters for :py:func:`pyteomics.pylab_aux.scatter_trend`
are `sigma_kwargs` and `sigma_values`.
- :py:mod:`pyteomics.pylab_aux` functions :py:func:`plot_line` and
:py:func:`scatter_trend` now return the objects they create.
- Writer functions (:py:func:`pyteomics.mgf.write`, :py:func:`pyteomics.fasta.write`,
:py:func:`pyteomics.fasta.write_decoy_db`) now accept a `file_mode` argument that
overrides the mode in which the file is opened.
- In :py:func:`pyteomics.mgf.write` one can now override the format spec for fragment m/z,
intensity and charge values using the optinal `fragment_format` argument. Key order and
key-value parameter formatters are now also handled via optional arguments.
- :py:func:`pyteomics.fasta.decoy_db` now supports `ignore_comments` and `parser` arguments.
3.1.1
-----
- Bugfix in :py:mod:`pyteomics.auxiliary`.
- New parameter `show_legend` in :py:func:`pyteomics.pylab_aux.scatter_trend`.
- Performance improvements in :py:mod:`pyteomics.parser`.
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
<http://dx.doi.org/10.1021/acs.jproteome.6b00144>`_).
- :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