Commit 6f89771c authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

Correct RST for pypi

parent 73bcfab7
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......@@ -16,7 +16,7 @@ Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-indu
:alt: Coverage Report
.. image:: https://readthedocs.org/projects/rapid-peptide-generator/badge/?version=latest
:target: http://rapid-peptide-generator.readthedocs.io/en/latest/?badge=latest
:target: https://rapid-peptide-generator.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
:note: RPG is tested with Gitlab Ci for the following Python version: 3.6 to 3.9
......@@ -44,7 +44,7 @@ Installation
In order to install RPG, you can use **pip**:
.. code-block:: none
.. code-block:: shell
pip3 install rpg
......@@ -56,6 +56,6 @@ Usage
From the command line:
.. code-block:: none
.. code-block:: shell
rpg --help
......@@ -8,13 +8,13 @@ Overview
You can run **Rapide Peptides Generator** using the standalone version called:
.. code-block:: none
.. code-block:: shell
rpg
You can obtain help by using:
.. code-block:: none
.. code-block:: shell
rpg --help
......@@ -27,13 +27,13 @@ From pip
The suggested way of installing the latest **RPG** version is through **pip**:
.. code-block:: none
.. code-block:: shell
pip3 install rpg
Then you can use:
.. code-block:: none
.. code-block:: shell
rpg --help
......@@ -42,7 +42,7 @@ From source code
**RPG** is coded in Python. To manually install it from source, get the source and install **RPG** using:
.. code-block:: none
.. code-block:: shell
git clone https://gitlab.pasteur.fr/nmaillet/rpg/
cd rpg
......@@ -69,7 +69,7 @@ To:
Then, from the main **RPG** directory, use:
.. code-block:: none
.. code-block:: shell
python3 rpg/RapidPeptidesGenerator.py -\\-help
......@@ -86,7 +86,7 @@ Getting help
To access build-in help, use:
.. code-block:: none
.. code-block:: shell
rpg -\\-help
......@@ -95,7 +95,7 @@ Listing enzymes
To list all available enzymes, use:
.. code-block:: none
.. code-block:: shell
rpg -l
......@@ -111,7 +111,7 @@ Sequential digestion of one sequence
To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and 5 and store results in `output_file.fasta`, use:
.. code-block:: none
.. code-block:: shell
rpg -s QWSDORESDF -o output_file.fasta -e 2 5
......@@ -122,7 +122,7 @@ Sequential digestion of a (multi)fasta file
To perform sequential digestion of `input_file.fasta` with enzymes 2 and 5 and store results in `output_file.fasta`, use:
.. code-block:: none
.. code-block:: shell
rpg -i input_file.fasta -o output_file.fasta -e 2 5
......@@ -131,7 +131,7 @@ Concurrent digestion of a (multi)fasta file
To perform concurrent digestion of `input_file.fasta` with enzymes 2 and 5 and store results in `output_file.fasta`, use:
.. code-block:: none
.. code-block:: shell
rpg -i input_file.fasta -o output_file.fasta -e 2 5 -d c
......@@ -140,7 +140,7 @@ Adding a new enzyme
To extend the list of the available enzymes and add a new one, use:
.. code-block:: none
.. code-block:: shell
rpg -a
......@@ -198,7 +198,7 @@ In concurrent mode, all enzymes are present at the same time during digestion an
Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after P. The second is called 'afterK' (id 29) and cleaves after K if there is no P just before. Digesting 'PKPKPKPK' using those two enzymes in sequential mode gives the following result (see :ref:`formats` for more information):
.. code-block:: none
.. code-block:: shell
$ rpg -s PKPKPKPK -e 28 29
>Input_0_afterP_1_1_115.13198_5.54
......@@ -218,7 +218,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the following result:
.. code-block:: none
.. code-block:: shell
$ rpg -s PKPKPKPK -e 28 29 -d c
>Input_0_afterP-afterK_1_1_115.13198_5.54
......@@ -252,7 +252,7 @@ Sometimes an enzyme does not cleave at a given position even if requirements are
For example, using:
.. code-block:: none
.. code-block:: shell
rpg -s QWSDORESDF -e 1 2 3 -m 1.4 2.6
......@@ -292,7 +292,7 @@ The isoelectric point is computed by solving Henderson–Hasselbalch equation us
The default output is in multi-fasta format. The header then summarizes all this information. For example, on the following multi-fasta result:
.. code-block:: none
.. code-block:: shell
>Input_0_Asp-N_3_3_419.43738_5.54
QWS
......@@ -321,7 +321,7 @@ Verbosity can be increased or decreased. The output file is not affected by **-v
With default verbosity level (no **-v** nor **-q** option), the output is:
.. code-block:: none
.. code-block:: shell
$ rpg -s QWSDORESDF -e 1
>Input_0_Asp-N_3_3_419.43738_5.54
......@@ -333,7 +333,7 @@ With default verbosity level (no **-v** nor **-q** option), the output is:
Increasing verbosity by one, *i.e.* using **-v**, adds information about used options. For example:
.. code-block:: none
.. code-block:: shell
$ rpg -s QWSDORESDF -e 1 -v
Warning: File 'peptides.fasta' already exit!
......@@ -353,7 +353,7 @@ Increasing verbosity by one, *i.e.* using **-v**, adds information about used op
Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about each of the digested proteins. For example:
.. code-block:: none
.. code-block:: shell
$ rpg -s QWSDORESDF -e 1 -vv
Warning: File 'peptides.fasta' already exit!
......@@ -382,7 +382,7 @@ Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about ea
Decreasing verbosity, *i.e.* using **-q** option, removes all information but errors. For example:
.. code-block:: none
.. code-block:: shell
$ rpg -s QWSDORESDF -e 1 -q
Warning: File 'peptides.fasta' already exit!
......@@ -399,13 +399,13 @@ Option **-a, -\\-addenzyme** allows the user to define new enzymes. An enzyme co
In the following, nomenclature of `Schechter and Berger <https://www.ncbi.nlm.nih.gov/pubmed/6035483>`_ is used. Amino acids before the cleavage site are designated as `P1`, `P2`, `P3`, etc in the N-terminal direction, and as `P1'`, `P2'`, `P3'`, etc in the C-terminal direction. For example, with cleavage site represented as '|':
.. code-block:: none
.. code-block:: shell
...P3-P2-P1-|-P1'-P2'-P3'...
In **RPG**, this nomenclature is represented as:
.. code-block:: none
.. code-block:: shell
...(P3)(P2)(P1)(,)(P1')(P2')(P3')...
......@@ -417,25 +417,25 @@ A rule specifies which amino acid is targeted by the enzyme, the cleavage positi
For example, to define a cleavage occurring **before** A, one must input:
.. code-block:: none
.. code-block:: shell
(,A)
To define a cleavage occurring **after** B, one must input:
.. code-block:: none
.. code-block:: shell
(B,)
The surrounding context is specified by adding other amino acids, before or after the targeted one. For example, to define a cleavage occurring **before** A, position `P1'`, preceded by B in position `P1`, C in position `P3` and followed by D in position `P2'`, one must input:
.. code-block:: none
.. code-block:: shell
(C)()(B)(,A)(D)
Note that this enzyme will only cleave if it finds the motif C*BAD, where * could be **any** amino acid. It will **not** cleave BAD, nor C*BA, BA, etc. For example, creating and using enzyme `rpg_example_userguide` (enzyme id 43):
.. code-block:: none
.. code-block:: shell
$ rpg -a
Name of the new enzyme?
......@@ -462,7 +462,7 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
In order for this enzyme to also cleave before AD (before A in `P1'` followed by D in `P2'` ), on top of the previous rule, one has to define one more rule in **RPG**:
.. code-block:: none
.. code-block:: shell
(,A)(D)
(C)()(B)(,A)(D)
......@@ -470,7 +470,7 @@ In order for this enzyme to also cleave before AD (before A in `P1'` followed by
It is important to note that for each enzyme, it is enough that one of the rule is broken for the cleavage to not occur. In this example, the defined enzyme will **not** cleave BAD, as it is specified that it will cleave before A preceded by B in `P1` **if there is C in `P3`**. Identically, it will **not** cleave C*BA*, as D is required in `P2'` for both rules.
.. code-block:: none
.. code-block:: shell
$rpg -a
Name of the new enzyme?
......@@ -506,14 +506,14 @@ It is important to note that for each enzyme, it is enough that one of the rule
The order of inputted rules is not relevant. In other words, this enzyme:
.. code-block:: none
.. code-block:: shell
(,A)(D)
(C)()(B)(,A)(D)
and this second one:
.. code-block:: none
.. code-block:: shell
(C)()(B)(,A)(D)
(,A)(D)
......@@ -522,7 +522,7 @@ are identical.
It is possible to define none-related cleavage rules for the same enzyme, for example:
.. code-block:: none
.. code-block:: shell
(G,)(G)
(P)(W,)(E)(T)
......@@ -531,13 +531,13 @@ This enzyme will cleave after G (position `P1`) followed by G in `P1'` and also
Note that each rule must concern only **one** cleavage site. It is not possible to input rule like:
.. code-block:: none
.. code-block:: shell
(A,)(B,)
This would define an enzyme cleaving after A in `P1` followed by B in `P1'` but also cleaving after B in `P1` preceded by A in `P2`. The proper way to input this is by using two separate rules:
.. code-block:: none
.. code-block:: shell
(A,)(B)
(A)(B,)
......@@ -552,19 +552,19 @@ An exception specifies when a cleavage should **not** occur. **Exceptions must a
For example, to define a cleavage occurring **before** A (`P1'` ), one must input:
.. code-block:: none
.. code-block:: shell
(,A)
Exceptions can then be inputted. For example, to define "a cleavage occurs before A, except when P is in `P2'` ", the following exception needs to be added:
.. code-block:: none
.. code-block:: shell
(,A)(P)
This enzyme will always cleave before A when not followed by P:
.. code-block:: none
.. code-block:: shell
rpg -a
Name of the new enzyme?
......@@ -594,13 +594,13 @@ This enzyme will always cleave before A when not followed by P:
It is possible to input complex exceptions. For the previous enzyme, we can add the following exception:
.. code-block:: none
.. code-block:: shell
(G)(T)()(,A)()(F)
This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` ) or preceded by G in `P3`, T in `P2`, by any amino acid in `P1` and `P2'`, and F in `P3'` **at the same time**:
.. code-block:: none
.. code-block:: shell
rpg -a
Name of the new enzyme?
......@@ -648,13 +648,13 @@ This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` )
It is important to understand that an exception should always be linked to a rule. If one inputs this rule:
.. code-block:: none
.. code-block:: shell
(A,)
followed by this exception:
.. code-block:: none
.. code-block:: shell
(B,)(C)
......@@ -671,26 +671,26 @@ To make enzyme creation easier to use, two tricks are available.
The first one simplifies the definition of enzymes cleaving **before** and **after** a given amino acid. Defining an enzyme cleaving, for example, before **and** after A, can be done with two rules:
.. code-block:: none
.. code-block:: shell
(,A)
(A,)
or simply using:
.. code-block:: none
.. code-block:: shell
(,A,)
The second trick is the use of the keyword `or`. This allows multiple possibilities for on position. For example:
.. code-block:: none
.. code-block:: shell
(,A or B)
is equivalent to:
.. code-block:: none
.. code-block:: shell
(,A)
(,B)
......@@ -701,7 +701,7 @@ Those two tricks help on complex enzymes. For example, :ref:`peps13` preferentia
It can be defined either by:
.. code-block:: none
.. code-block:: shell
cleaving rules:
......@@ -737,7 +737,7 @@ It can be defined either by:
or, in a condensed way:
.. code-block:: none
.. code-block:: shell
cleaving rule:
......
......@@ -140,7 +140,7 @@ setup(
#
# For an analysis of "install_requires" vs pip's requirements files see:
# https://packaging.python.org/en/latest/requirements.html
install_requires=[''], # Optional
#install_requires=[''], # Optional
# List additional groups of dependencies here (e.g. development
# dependencies). Users will be able to install these using the "extras"
......
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