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Diffstat (limited to 'CHANGELOG')
| -rw-r--r-- | CHANGELOG | 86 |
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diff --git a/CHANGELOG b/CHANGELOG index 77c44243f0ae..fd49134a727c 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,89 @@ +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 ----- |