Skip to main content

A RNAVIEW parser

Project description

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

.. _RNAVIEW: .. _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:


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()
| 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)
 [BasePair(orientation='cis', position_1=1, position_2=72, base_1='G', base_2='C', interaction_type='+/+')])

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

rnaviewparser-0.1.3.tar.gz (6.3 kB view hashes)

Uploaded source

Built Distribution

rnaviewparser-0.1.3-py3-none-any.whl (8.2 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page