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A RNAVIEW parser

Project description

rnaviewparser is a simple parser for RNAVIEW_ filename.pdb.out files.

.. _RNAVIEW: http://ndbserver.rutgers.edu/ndbmodule/services/download/rnaview.html .. _ply: https://www.dabeaz.com/ply/"

It uses ply_ for the lexing/parsing bit and python dataclasses to store the data. It allows an export to CSV files.

It works with Python 3.7.

:Author: Maria Climent-Pommeret (Chopopope) :License: MIT License :Homepage: https://gitlab.climent-pommeret.red/Chopopope/rnaviewparser

Installating

Please install in a virtual environment that uses Python3.7 by typing::

pip install rnaviewparser

Usage example

Consider this::

In[1]: from rnaviewparser import rnaviewparser

In[2]: basepairs = rnaviewparser.RnaviewParser("~/playground/tr0001.pdb.out").parse()

In[3]: factory = basepairs.generate_interactions()

In[4]: wh = factory["W/H"]

In[5]: wh.pretty()
Out[5]:
+------------------+-------------+-------+
| Interaction type | Orientation | Total |
+------------------+-------------+-------+
|       std        |     cis     |   0   |
|       std        |    trans    |   0   |
+------------------+-------------+-------+

In[6]: basepairs.csv("/tmp/foo.csv")

In[7]: ww = factory["W/W"]

In[8]: ww.find_interaction_by_position(8)
Out[8]:
(1,
 [BasePair(orientation='cis', position_1=1, position_2=72, base_1='G', base_2='C', interaction_type='+/+')])


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