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Documentation typo fixes
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veghp committed Sep 10, 2020
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Expand Up @@ -83,16 +83,16 @@ attempt to find larger sets:
Finding a sequence decomposition
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


In this example, we find where to cut a 50-kilobasepair sequence to create
assemblable fragments with 4-basepair overhangs. We indicate that:

- There should be 50 fragments, with a minimum of variance in their sizes.
- The fragments overhangs should have 25-75 GC% with a 1-basepair difference
between any two overhangs (and their reverse-complement). They should also be
compatible with the 4-basepair extremities of the sequence.
between any two overhangs (and their reverse-complement). They should also be
compatible with the 4-basepair extremities of the sequence.

.. code:: python
Expand All @@ -104,7 +104,7 @@ assemblable fragments with 4-basepair overhangs. We indicate that:
solution = selector.cut_sequence(sequence, equal_segments=50,
max_radius=20, include_extremities=True)
This returns a list of dictionnaries, each representing one overhang with
This returns a list of dictionaries, each representing one overhang with
properties ``o['location']`` (coordinate of the overhang in the sequence)
and ``o['sequence']`` (sequence of the overhang).

Expand All @@ -123,7 +123,7 @@ the overhang's positions, using the following function:
display_positions=False)
Sequence mutation and decomposition from a Genbank file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

If the input sequence is a Genbank record (or a Biopython record) has locations
annotated vy features feature labeled ``!cut``, GoldenHinges will attempt to
Expand All @@ -135,7 +135,7 @@ Note that solutions involving base changes are penalized and solutions involving
the original solution will always be prefered, so no base change will be
suggested unless strictly necessary.

If the input record has `DnaChisel <https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_
If the input record has `DNA Chisel <https://github.com/Edinburgh-Genome-Foundry/DnaChisel>`_
annotations such as ``@AvoidChanges`` or ``@EnforceTranslation``, these will be
enforced to forbid some mutations.

Expand Down Expand Up @@ -180,13 +180,13 @@ using this command:
Contribute !
--------------
------------

Golden Hinges is an open-source software originally written at the
`Edinburgh Genome Foundry <http://edinburgh-genome-foundry.github.io/home.html>`_
by `Zulko <https://github.com/Zulko>`_ and
`released on Github <https://github.com/Edinburgh-Genome-Foundry/GoldenHinges>`_
under the MIT licence. Everyone is welcome to contribute !
under the MIT licence. Everyone is welcome to contribute!

.. raw:: html

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