crazydoc

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<img alt="crazydoc Logo" title="crazydoc Logo" src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/crazydoc/master/docs/title.png" width="550">
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Crazydoc is a Python library to parse one of the most common DNA representation formats: the joyfully coloured and stylishly annotated MS-Word document.

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Crazydoc returns Biopython records of the sequences contained in an MS-Word document, with record features corresponding to the various sequence highlightings (background color, boldness, italics, case change, etc.). The records can saved as GenBanks or easily plotted.

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Motivation

While other standards such as FASTA or Genbank are better supported by modern sequence editors, none enjoys the same popularity among molecular biologist as MS-Word's .docx format, which is limited only by the sophistication and creativity of the user.

Relying on a loose syntax and unclear specifications, this format has however suffered from a lack of support in the developers community and is generally incompatible with mainstream software pipelines. This library allows to convert MS-Word DNA sequences to more computing friendly formats: Biopython records, FASTA, or annotated Genbanks.

Usage

To obtain all sequences contained in a docx as annotated Biopython records (such as this one <https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/crazydoc/master/examples/example.docx>_):

.. code:: python

from crazydoc import CrazydocParser
parser = CrazydocParser(['highlight_color', 'bold', 'underline'])
biopython_records = parser.parse_doc_file("./example.docx")

You can then plot the obtained records:

.. code:: python

from crazydoc import CrazydocSketcher
sketcher = CrazydocSketcher()
for record in biopython_records:
    sketch = sketcher.translate_record(record)
    ax, _ = sketch.plot()
    ax.set_title(record.id)
    ax.figure.savefig('%s.png' % record.id)

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<img src="https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/crazydoc/master/docs/records_plots.png" width="800">
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To write the sequences down as Genbank records, with annotations:

.. code:: python

from crazydoc import records_to_genbank
records_to_genbank(biopython_records)

Note that records_to_genbank() will truncate the record name to 20 characters, to fit in the GenBank format. Additionally, slashes (/) will be replaced with hyphens (-) in the filenames. To read protein sequences, pass is_protein=True:

.. code:: python

biopython_records = parse_doc_file(protein_path, is_protein=True)

This will return protein records, which will be saved with a GenPept extension (.gp) by records_to_genbank(biopython_records, is_protein=True), unless specified otherwise with extension=.

You can also save annotated sequences as colourful Word docs. write_crazydoc() takes a SeqRecord, the qualifier key to use as a feature name, and a path to save the document to.

.. code:: python

# Load an annotated sequence with Biopython
from Bio import SeqIO
from crazydoc import write_crazydoc
seq = SeqIO.read("examples/examples_outputs/Sequence 1.gbk", "genbank")
# Most features will already have some name qualifier but you can add your own
for i,f in enumerate(seq.features):
    f.qualifiers['product'] = f"feature{i}"
# Save the annotated sequence as a docx
write_crazydoc(seq, 'product', 'test.docx')

Installation

You can install crazydoc through PIP:

.. code::

pip install crazydoc

Alternatively, you can unzip the sources in a folder and type:

.. code::

python setup.py install

License = MIT

Crazydoc is an open-source software originally written at the Edinburgh Genome Foundry <http://genomefoundry.org>_ by Zulko <https://github.com/Zulko>_ and released on Github <https://github.com/Edinburgh-Genome-Foundry/crazydoc>_ under the MIT licence (Copyright 2018 Edinburgh Genome Foundry).

Everyone is welcome to contribute!

More biology software

.. image:: https://raw.githubusercontent.com/Edinburgh-Genome-Foundry/Edinburgh-Genome-Foundry.github.io/master/static/imgs/logos/egf-codon-horizontal.png :target: https://edinburgh-genome-foundry.github.io/

Crazydoc is part of the EGF Codons <https://edinburgh-genome-foundry.github.io/>_ synthetic biology software suite for DNA design, manufacturing and validation.