thomashsmith / phosphoprotools

Phosphoprotools

Collection of functions for processing phosphoproteomics data, including:

• Annotate phospho-sites using PhosRS cutoff value
• Retrieve Gene/Protein synonyms from Uniprot
• Annotate previously reported phospho-sites (as reported by PhosphoSitePlus database)
• Annotate functional phospho-sites (as reported by PhosphoSitePlus database)
• Statistical analysis by pi-score method for differential phosphopeptide abundance between two groups
• Retrieve publication counts for genes with desired keywords

Getting Started

Python Requirements

• Python 2.7 with the following packages:
• Pandas
• Tqdm
• numpy
• scipy.stats

Aside from Tqdm, all of these are included in the Anaconda distribution of Python 2.7 (https://www.continuum.io/downloads). Missing packages should be installed automatically as part of the pip install of the phosphoprotools package.

Installation

pip install phosphoprotools

Other Requirements

For annotation of known/functional phosphosites, you will need to download three files from the PhosphoSitePlus database (http://www.phosphosite.org/staticDownloads.action). After registering for a free account, download the following files to your Desktop.

• Phosphorylation_site_dataset.gz (all reported functional sites)
• Phosphosite_seq.fasta.gz (reference sequences)
• Regulatory_sites.gz (all reported functional sites)

When phosphoprotools is imported for the first time, the above three compessed files will be automaticallly extracted to the package /data directory and saved as a .pickle. After first import the files downloaded to your Desktop can be deleted.

PhosphoProTools
├── LICENSE
├── MANIFEST.in
├── README.md
├── setup.py
└── src
    └── phosphoprotools
        ├── __init__.py
        ├── data
        │   ├── Phosphorylation_site_dataset.pickle
        │   ├── Phosphosite_seq.fasta.pickle
        │   └── Regulatory_sites.pickle
        ├── piscoreanalysis.py
        ├── preprocessing.py
        ├── pubfetch.py
        ├── siteannotation.py
        └── synonymsfetch.py

TODO

• Finish up comments

• Add example ipynb

• Add sample data for testing

• Add easy command to update db pickels

• • Add reference sequences pickle that is permanently saved/updates self

• Workaround for long link problem (Excel's 255 character limit)

• Add synonynms df pickle that is permanently saved, updates self [0.18]

• Add pubcount column with number only [0.16]

• fix publication fetch error when only searching 3 terms [0.16]

• remove [TIAB] from each term!!!!!! [0.16]

• Add n-mer sequence motif output (for motif analysis) [0.19]

Authors

• Thomas Smith - ThomasHSmith

License

This work is licensed under the MIT License - see LICENSE.md for details.