diff options
-rw-r--r-- | .SRCINFO | 8 | ||||
-rw-r--r-- | CHANGELOG | 43 | ||||
-rw-r--r-- | PKGBUILD | 4 |
3 files changed, 48 insertions, 7 deletions
@@ -1,8 +1,6 @@ -# Generated by makepkg 4.2.1 -# Wed Apr 15 22:17:40 UTC 2015 pkgbase = python-pyteomics pkgdesc = A framework for proteomics data analysis. - pkgver = 3.0.1 + pkgver = 3.1 pkgrel = 1 url = http://pythonhosted.org/pyteomics changelog = CHANGELOG @@ -13,8 +11,8 @@ pkgbase = python-pyteomics optdepends = python-lxml: for XML parsing modules, recommended optdepends = python-numpy: for lots of features, highly recommended options = !emptydirs - source = https://pypi.python.org/packages/source/p/pyteomics/pyteomics-3.0.1.tar.gz - md5sums = 2c838cc1c16dce69148662b883c755b9 + source = https://pypi.python.org/packages/source/p/pyteomics/pyteomics-3.1.tar.gz + md5sums = 5e4c8d38f0891e82b8ec30515ce6718f pkgname = python-pyteomics diff --git a/CHANGELOG b/CHANGELOG index a9f2bb997e99..7dcb0ee07f39 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,3 +1,45 @@ +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 ----- @@ -8,6 +50,7 @@ 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. @@ -1,6 +1,6 @@ # Maintainer: Lev Levitsky <levlev at mail dot ru> pkgname=python-pyteomics -pkgver=3.0.1 +pkgver=3.1 pkgrel=1 pkgdesc="A framework for proteomics data analysis." arch=('any') @@ -12,7 +12,7 @@ optdepends=('python-matplotlib: for pylab_aux module, optional' \ 'python-numpy: for lots of features, highly recommended') options=(!emptydirs) source=("https://pypi.python.org/packages/source/p/pyteomics/pyteomics-${pkgver}.tar.gz") -md5sums=('2c838cc1c16dce69148662b883c755b9') +md5sums=('5e4c8d38f0891e82b8ec30515ce6718f') changelog="CHANGELOG" package() { cd "${srcdir}/pyteomics-${pkgver}" |