monoseq is a Python library for pretty-printing sequence strings using a
monospace font. It also provides a simple command line interface.
Sequences are pretty-printed in the for DNA and proteins traditional way using blocks of letters where each line is prefixed with the sequence position. User-specified regions are highlighted using different formatting styles. The output format can be HTML or plaintext with optional styling using ANSI escape codes for use in a terminal.
>>> import monoseq
>>> sequence = 'MIMANQPLWLDSEVEMNHYQQSHIKSKSPYFPEDKHICWIKIFKAFGT' * 4
>>> print monoseq.pprint_sequence(sequence, mode='plaintext')
1 MIMANQPLWL DSEVEMNHYQ QSHIKSKSPY FPEDKHICWI KIFKAFGTMI MANQPLWLDS
61 EVEMNHYQQS HIKSKSPYFP EDKHICWIKI FKAFGTMIMA NQPLWLDSEV EMNHYQQSHI
121 KSKSPYFPED KHICWIKIFK AFGTMIMANQ PLWLDSEVEM NHYQQSHIKS KSPYFPEDKH
181 ICWIKIFKAF GTThis screenshot shows the use of ANSI escape codes:
Here is an example of monoseq used to output
HTML, and this IPython Notebook
shows how to pretty-print sequences in an IPython Notebook.
To install the latest release via PyPI using pip:
pip install monoseq
The latest documentation with user guide and API reference is hosted at Read The Docs.
You can also compile the documentation directly from the source code by
running make html from the doc/ subdirectory. This requires
Sphinx to be installed.
monoseq is licensed under the MIT License, see the LICENSE.rst file
for details. See the AUTHORS.rst file for a list of authors.