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14 changes: 7 additions & 7 deletions README.rst
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Expand Up @@ -54,7 +54,7 @@ Please cite this paper_.
Installation:
-------------

It is recommended to install pyGeno within a `virtual environement`_, to setup one you can use:
It is recommended to install pyGeno within a `virtual environment`_, to setup one you can use:

.. code:: shell

Expand Down Expand Up @@ -129,7 +129,7 @@ Should output:

Creating a Personalized Genome:
-------------------------------
Personalized Genomes are a powerful feature that allow you to work on the specific genomes and proteomes of your patients. You can even mix several SNP sets together.
Personalized Genomes are a powerful feature that allows you to work on the specific genomes and proteomes of your patients. You can even mix several SNP sets together.

.. code:: python

Expand Down Expand Up @@ -249,7 +249,7 @@ To get a list of remote datawraps that pyGeno can download for you, do:
Importing whole genomes is a demanding process that take more than an hour and requires (according to tests)
at least 3GB of memory. Depending on your configuration, more might be required.

That being said importating a data wrap is a one time operation and once the importation is complete the datawrap
That being said importing a data wrap is a one time operation and once the importation is complete the datawrap
can be discarded without consequences.

The bootstrap module also has some handy functions for importing built-in packages.
Expand All @@ -265,7 +265,7 @@ Some of them just for playing around with pyGeno (**Fast importation** and **Sma
B.importGenome("Human.GRCh37.75_Y-Only.tar.gz")

#A dummy datawrap for humans SNPs and Indels in pyGeno's AgnosticSNP format.
# This one has one SNP at the begining of the gene SRY
# This one has one SNP at the beginning of the gene SRY
B.importSNPs("Human.dummySRY_casava.tar.gz")

And for more **Serious Work**, the whole reference genome.
Expand Down Expand Up @@ -361,13 +361,13 @@ Find in sequences:
------------------

Internally pyGeno uses a binary representation for nucleotides and amino acids to deal with polymorphisms.
For example,both "AGC" and "ATG" will match the following sequence "...AT/GCCG...".
For example, both "AGC" and "ATG" will match the following sequence "...AT/GCCG...".

.. code:: python

#returns the position of the first occurence
#returns the position of the first occurrence
transcript.find("AT/GCCG")
#returns the positions of all occurences
#returns the positions of all occurrences
transcript.findAll("AT/GCCG")

#similarly, you can also do
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