Pout2prot

Release 1.2.1 of the pout2prot package fixes a bug that caused some of the subgroups to be identified incorrectly. Please upgrade to this release in order to be assured that all subgroups will be found correctly.

This release of the `pout2prot` CLI changes the way the input is presented to the script and fixes a few important bugs that caused the subgrouping to return wrong results in certain situations.

**Enhancements:**
* The input parameter for the command behaves differently from now on. This input argument should now point to either (i) a single *.pout file, (ii) a folder that contains one or more *.pout files, or (ii) a parent folder with subfolders containing *.pout files in the case there are different sample categories. In the latter case, the --sample_categories option should be used.

**Bug fixes:**
* Fixed bug that caused the subgrouping algorithm to produce wrong results in specific situations.

Version 1.1.0 of the pout2prot package provides one extra command line argument and fixes a few bugs.

**Enhancements:**
* Added `sample_categories` CLI option. Before, if the input-folder given as argument to the command contained subfolders, it interpreted each subfolder as one sample category and all `.pout`-files in this subfolder were then linked to this category. This behaviour has changed and will now only be applied when the `--sample_categories` CLI-option is passed to the command.

**Bug fixes:**
* The `decoy_flag` parameter is now empty by default. Before this, it was not possible to disable the decoy-filtering.

This release contains only one minor improvement of the documentation of the tool.

**Bug fixes / Improvements:**
* Default FDR-value is now also mentioned in the help information of the command line tool for pout2prot.

This is the first fully stable release of the `pout2prot` package, which can be found on [PyPi](https://pypi.org/project/pout2prot/). See our [readme](https://github.com/tivdnbos/pout2prot) for more information on how to use this package.