diff options
Diffstat (limited to 'CHANGELOG')
-rw-r--r-- | CHANGELOG | 73 |
1 files changed, 70 insertions, 3 deletions
diff --git a/CHANGELOG b/CHANGELOG index ae7bcfd51f05..7dd20f84991e 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,61 @@ +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 ----- @@ -84,7 +142,8 @@ New submodule :py:mod:`pyteomics.featurexml` with a parser for OpenMS **featureX - 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. + - 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 ........... @@ -294,23 +353,30 @@ Fix for a memory leak in :py:func:`pyteomics.mzid.get_by_id`, which affects - 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. @@ -520,7 +586,7 @@ Bugfixes: 2.1.2 ----- - - Bugfix in XML parsers. The bug caused the mzML parser break on some files. + - Bugfix in XML parsers. The bug caused the mzML parser to break on some files. The fix can slightly change the format of the output. 2.1.1 @@ -671,7 +737,8 @@ API changes ----- - Bugfix in :py:mod:`pyteomics.pepxml`: modification info is now extracted. - - New optional bool argument 'split' in :py:func:`pyteomics.parser.parse_sequence()` + + - New optional boolean 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 |