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<p><b>Requirements for API:</b></p>
1. Python<br>
<p>
To use PON-P2 API, you need python installed in your computer. Python is pre-installed on most Linux distributions and MAC OS X.
For Windows, you can download python from <a href="https://www.python.org/downloads/windows/">python.org</a>.
</p><br>
2. SUDS client for SOAP<br>
<p>
We use Simple Object Access Protocol (SOAP) to provide PON-P2 API.
To connect with PON-P2 API, you need to install Suds web services client from <a href="https://pypi.python.org/pypi/suds">here</a>.
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3. PON-P2 API client script<br>
<p>
We have prepared a python script to submit variants in VCF file and receive PON-P2 predictions in a text file. You can download the script from here.<br>
<a href="{% url 'ponp.views.clientDownload' %}">Download python script to run PON-P2 API</a>
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<p><b>Variation submission</b></p>
<p>
PON-P2 API accepts variant submission in VCF file only.
The program requires at least the first line in the VCF file starting with '##fileformat=VCFv' and the first five columns of the 'header line' and the 'data lines'.
When a VCF file is submitted, the program preprocesses the file and submits only single nucleotide substitutions for prediction.
Very big files can take long time to upload and the process may break.
Therefore, the VCF file is splitted into smaller files of approximately 20 MB and they are submitted to PON-P2.
<br><br>
To submit variants in a VCF file by using the API, run the following command:<br><br><br>
<font color="red">python PON-P2_API_client.py inputFile.vcf hg19 output/directory/path</font><br><br><br>
<font color="red">PON-P2_API_client.py:</font> The downloaded python script from this page.<br>
<font color="red">inputFile.vcf:</font> Complete path to the input VCF file. The file must contain the first line in a VCF file. Read more about VCF file <a href="http://samtools.github.io/hts-specs/VCFv4.1.pdf" style="text-decoration:none">here</a> or <a href="http://samtools.github.io/hts-specs/VCFv4.2.pdf" style="text-decoration: none">here</a>.<br>
<font color="red">genome assembly:</font> Either hg19 or hg38.<br>
<font color="red">output/directory/path:</font> Complete path to the directory where the results should be saved.<br>
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<p><b>PON-P2 results file</b></p>
<p>
After submitting the variants in the VCF file, the jobs are queued in the PON-P2 queue system.
When the predictions for the submitted jobs are completed, the results are saved in a file in the output directory.
If the input file is too big, there will be more than one results file, one for each jobid and one combined result file.
The combined result file contains two parts:<br><br>
1) Information section<br>
This section contains information about PON-P2.
Each line in this section starts with #.
<br><br>
2) Prediction section<br>
This section contains the results of PON-P2 prediction for variants leading to amino acid substitutions.
The first line of this section contains the column names and the subsquent lines contain prediction for one variation each.

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