signalPclient is small Python module that automates the submission of a sequence databank to SignalP 4.1 Server, a web service that detects and predicts the cleavage points of signal peptides for Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. SignalP Server is hosted by the Center for Biological Sequence Analysis at the Technical University of Denmark (DTU):
http://www.cbs.dtu.dk/services/SignalP/
We started developing signalPclient during the Python Hackathon, hosted by the QCB Collaboratory at UCLA. SignalP Server was originally proposed on a Nature Methods paper by TN Petersen, S Brunak, G von Heijne and H Nielsen.
If you have pip, you can install signalPclient using:
pip install git+https://github.com/QCB-Collaboratory/signalPclient
Otherwise, you can download signalPclient and use run its setup script. To download it, simply click here. After unzipping the file, navigate to the unzipped signalPclient directory and run:
python setup.py install
If you have a fasta file databank.fasta with sequences that you want to submit to SignalP Server, run:
import signalPclient
SPclient = signalPclient( input='databank.fasta', output='signalP.fasta' )
SPclient.submit()
If you have questions, comments or found a bug in our script, feel free to open an issue on the Issues Page. Also, feel free to submit Pull Requests in case you have modified the script to enhance or improve it.
signalPclient has minimal requirements, and works with both Python 2 or 3. Other than the standard Python libraries, signalPclient only requires:
- pyfasta
- MechanicalSoup
- Thiago Mosqueiro
- Xiaofei Lin
- Anela Tosevska
- Cheng Chen
- João VD Molino
Feel free to use/share/modify/redistribute this Python script, which is shared under the MIT license. This is a short and permissive license with conditions only requiring preservation of copyright and license notices. Licensed works, modifications, and larger works may be distributed under different terms and without source code.