citable release

Creating a release version of this software that can be cited

GUI with bug fixes

Differently from the previous release this version has many fixed bugs. Several of these bugs include: ensuring that the happy flow is retained even if no identifiers are found in the fasta headers, ensuring that the program doesn't crash whenever something goes wrong while clustering or a bad request is gained from uniprot and the program is able to cluster large amounts of proteins instead of getting a recursion error.

Additionally, fixed a semantic error where the program checks whether the output file already exists and if this is not the case the program quits. This behavior has been changed to the program checking whether the directory location if present is a directory.
Furthermore, changed the behavior of the mitocarta step. A different implementation is used to examine whether a protein is present in mitocarta resulting in fewer but more relevant results. Also, I removed the option to select which organism to select in mitocarta.

Lastly, I enabled the option to determine in which order the original columns of the maxquant file are written away and the samples are ordered alphabetically.

Release with GUI

This version has a Graphical User Interface (GUI) which makes it miles more user friendly than the program was. In the README it is described how the program works. Furthermore, this version differently from the previous versions has some changes to its behaviour and has more functionality to make the program more robust.

stable release 1.0

Several changes have been made in this release. Several semantic bugs have been fixed: (1) a bug where the applying and non_applying rows where refreshed per protein_filter has been changed and (2) the gene name is processed in the correct way. Additionally, there are multiple gene and protein names so a list has been made with the gene and protein names found in the uniprot so far which can be updated by the user. Furthermore, each protein found in uniprot is not displayed anymore, only when errors occur. Lastly, the order in which columns are written away to to the excel file has been changed so that the first column is a header column which can be defined by the user.

stable initial release

The additions to this release are (1) filtered away columns are not retained but filtered away rows because these rows represents proteins that might have been of interest and (2) a single executable has been created instead of one directory.

"It works for me" release

As the title of this release says, 'the executable works for me'. The program is in such a stage that the code and the executable give comparable results on my computer. Anyway, the 'process_maxquant_executable.exe' should be able to process a maxquant file on a windows machine with the settings file and maxquant output file.

Initial release

Process_maxquant.py is a script that processes the output of a maxquant file. Using pyinstaller 4.3 an executable has been made of process_maxquant.py If I am correct (and I am probably not) the created .spec file can be used by other people to use process_maxquant.py without having to install python.