diff --git a/README.rst b/README.rst
index 30ef9190e5e4fcd3de128c40f486576aa391f308..ebae70fb907c8765a0ddb142e2011dd7f9e4167a 100644
--- a/README.rst
+++ b/README.rst
@@ -1,7 +1,7 @@
RapidPeptidesGenerator (RPG)
============================
-Rapid Peptides Generator (RPG) is dedicated to predict proteases-induced cleavage sites on amino acid sequences.
+Rapid Peptides Generator (RPG) is a software dedicated to predict proteases-induced cleavage sites on amino acid sequences.
.. image:: https://badge.fury.io/py/rpg.svg
:target: https://badge.fury.io/py/rpg
@@ -29,13 +29,13 @@ Overview
Rapid Peptides Generator (RPG), is a standalone software dedicated to predict proteases-induced cleavage sites on sequences.
-RPG is a python tool taking (multi-)fasta/fastq file of proteins as input and digest each of them. Digestion mode can be either 'concurrent', i.e. all enzymes are present at the same time during digestion, or 'sequential'. In sequential mode, each protein will be digested by each enzyme, one by one.
+RPG is a python tool taking a (multi-)fasta/fastq file of proteins as input and digest each of them. The digestion mode can be either 'concurrent', i.e. all enzymes are present at the same time during digestion, or 'sequential'. In sequential mode, each protein will be digested by each enzyme, one by one.
The resulting peptides contain informations about positions of cleavage site, peptide sequences, length, mass as-well as an estimation of isoelectric point (pI) of each peptide. Shortly, the isoelectric point is the pH at which a peptide carries no net electrical charge and a good approximation can be computed on small molecules. Results are outputted in multi-fasta, CSV or TSV file.
-Currently, 42 enzymes and chemicals are included in RPG. User can easily design new enzymes, using a simple yet powerful grammar. This grammar allows the user to design complex enzymes like trypsin or thrombin, including many exceptions and different cleavage sites. User-defined enzymes are then interpreted by RPG and included in the local installation of the software.
+Currently, 42 enzymes and chemicals are included in RPG. The user can easily design new enzymes, using a simple yet powerful grammar. This grammar allows the user to design complex enzymes like trypsin or thrombin, including many exceptions and different cleavage sites. User-defined enzymes are then interpreted by RPG and included in the local installation of the software.
-RPG follows the standards for software development with continuous integration on Gitlab (https://gitlab.pasteur.fr/nmaillet/rpg) and automatic on-line documentation (https://rapid-peptide-generator.readthedocs.io).
+RPG follows the standards for software development with continuous integration on Gitlab (https://gitlab.pasteur.fr/nmaillet/rpg) and automatic on-line documentation (https://rapid-peptide-generator.readthedocs.io).
@@ -46,7 +46,7 @@ In order to install RPG, you can use **pip**:
.. code-block:: none
- pip install rpg
+ pip3 install rpg
This command installs RPG and its Python dependencies.
diff --git a/docs/userguide.rst b/docs/userguide.rst
index 2faf2402865896496d238156931e3af7bfd27d64..51391a1836934d862bca8bb3b896fb3baf2ea290 100644
--- a/docs/userguide.rst
+++ b/docs/userguide.rst
@@ -6,7 +6,7 @@ User Guide
Overview
========
-You can run **Rapide Peptide Generator** using the standalone called:
+You can run **Rapide Peptide Generator** using the standalone version called:
.. code-block:: none
@@ -16,7 +16,7 @@ You can obtain help by using:
.. code-block:: none
- rpg --help
+ rpg -\\-help
Installation
@@ -29,18 +29,18 @@ The suggested way of installing the latest **RPG** version is through **pip**:
.. code-block:: none
- pip install rpg
+ pip3 install rpg
Then you can use:
.. code-block:: none
- rpg --help
+ rpg -\\-help
From source code
----------------
-**RPG** is coded in Python. To manually install it from sources, get the source and install **RPG** using:
+**RPG** is coded in Python. To manually install it from source, get the source and install **RPG** using:
.. code-block:: none
@@ -48,12 +48,14 @@ From source code
cd rpg
python setup.py install
-Using without installing
-------------------------
+Using without installation
+--------------------------
+
+You can download the source code from Pasteur's **Gitlab**: https://gitlab.pasteur.fr/nmaillet/rpg/.
-You can download source code in Pasteur's **Gitlab**: https://gitlab.pasteur.fr/nmaillet/rpg/.
+In order to directly run **RPG** from source, you need to copy file ``tests/context.py`` into ``rpg`` folder.
-In order to directly run **RPG** from sources, you need to uncomment line 42 of ``rpg/RapidePeptideGenerator.py``. Modify:
+Then, uncomment line 42 of ``rpg/RapidePeptideGenerator.py``. Modify:
.. code-block:: python
@@ -65,19 +67,19 @@ To:
from context import rpg
-Then, from main **RPG** directory, use:
+Then, from the main **RPG** directory, use:
.. code-block:: none
- python3 rpg/RapidPeptidesGenerator.py --help
+ python3 rpg/RapidPeptidesGenerator.py -\\-help
-.. warning:: It not recommended, as you need all requirements of `requirements.txt` installed locally and you may encounter issues with Sphinx autodoc or other unwanted behaviors.
+.. warning:: Using without installation is not recommended, as you need all requirements of `requirements.txt` installed locally and you may encounter issues with Sphinx autodoc or other unwanted behaviors.
Classical use
=============
-Here are classical ways to use **RPG**.
+Here are some typical examples of **RPG** usage.
Getting help
------------
@@ -86,7 +88,7 @@ To access build-in help, use:
.. code-block:: none
- rpg --help
+ rpg -\\-help
Listing enzymes
---------------
@@ -100,7 +102,7 @@ To list all available enzymes, use:
Performing digestion
--------------------
-There is two digestion modes in **RPG**. In sequential mode, each protein will be digested by each enzyme, one by one. In concurrent mode, all enzymes are present at the same time during digestion. See :ref:`digestion` for more informations.
+There are two digestion modes in **RPG**. In sequential mode, each protein will be digested by each enzyme, one by one. In concurrent mode, all enzymes are present at the same time during digestion. See :ref:`digestion` for more information.
.. _oneseq:
@@ -134,45 +136,47 @@ To perform concurrent digestion of `input_file.fasta` with enzymes 2 and 5 and s
Adding a new enzyme
-------------------
-To add a new enzyme, use:
+To extend the list of the available enzymes and add a new one, use:
.. code-block:: none
rpg -a
+See :ref:`addenzyme` for more information.
+
Options
=======
Here are all available options in **RPG**:
-**-h, --help**: show this help message and exit.
+**-h, -\\-help**: Show this help message and exit.
-**-a, --addenzyme**: Add a new user-defined enzyme. See :ref:`addenzyme` for more informations.
+**-a, -\\-addenzyme**: Add a new user-defined enzyme. See :ref:`addenzyme` for more information.
-**-d, --digest**: Digestion mode. Either 's', 'sequential', 'c' or 'concurrent' (default: s). See :ref:`digestion` for more informations.
+**-d, -\\-digest**: Digestion mode. Either 's', 'sequential', 'c' or 'concurrent' (default: s). See :ref:`digestion` for more information.
-**-e, --enzymes**: Id of enzyme(s) to use (i.e. -e 0 -e 5 -e 10 to use enzymes 0, 5 and 10). Use -l first to get enzyme ids. See :ref:`enzymes` for more informations.
+**-e, -\\-enzymes**: Enzyme(s) id number to use (*i.e.* -e 0 -e 5 -e 10 to use enzymes 0, 5 and 10). Use -l first to get enzyme ids. See :ref:`enzymes` for more information.
-**-f, --fmt**: Output file format. Either 'fasta', 'csv', or 'tsv' (default: fasta). See :ref:`formats` for more informations.
+**-f, -\\-fmt**: Output file format. Either 'fasta', 'csv', or 'tsv' (default: fasta). See :ref:`formats` for more information.
-**-i, --inputdata**: Input file, in (multi)fasta / fastq format or a single protein sequence without commentary. See :ref:`oneseq` for example.
+**-i, -\\-inputdata**: Input file, in (multi)fasta / fastq format or a single protein sequence without commentary. See :ref:`oneseq` for example.
-**-l, --list**: Display the list of available enzymes.
+**-l, -\\-list**: Display the list of available enzymes.
-**-m, --misscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order than -enzymes options (i.e. -m 15 -m 5 -m 10). Only for sequential digestion (default: 0). See :ref:`misscleavage` for more informations.
+**-m, -\\-misscleavage**: Percentage of miscleavage, between 0 and 100, by enzyme(s). It should be in the same order as the -\\-enzymes options (*i.e.* -m 15 -m 5 -m 10). It works only for sequential digestion (default: 0). See :ref:`misscleavage` for more information.
-**-n, --noninteractive**: Non-interactive mode. No standard output, only error(s) (--quiet enable, overwrite -v). If output filename already exists, output file will be overwritten. See :ref:`nointer` for more informations.
+**-n, -\\-noninteractive**: Non-interactive mode. No standard output, only error(s) (-\\-quiet enable, overwrite -v). If output filename already exists, output file will be overwritten. See :ref:`nointer` for more information.
-**-o, --outputfile**: Result file to output result peptides (default './peptides.xxx' depending of --fmt).
+**-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt).
-**-r, --randomname**: Random (not used) output name file. See :ref:`random` for more informations.
+**-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.
-**-q, --quiet**: No standard output, only error(s).
+**-q, -\\-quiet**: No standard output, only error(s).
-**-v, --verbose**: Increase output verbosity. -vvv will increased more than -vv or -v. See :ref:`verbose` for more informations.
+**-v, -\\-verbose**: Increase output verbosity. -vv will increased more than -v. See :ref:`verbose` for more information.
-**--version**: show program's version number and exit.
+**-\\-version**: Show program's version number and exit.
.. _digestion:
@@ -180,11 +184,11 @@ Here are all available options in **RPG**:
Digestion modes
===============
-There is two digestion modes in **RPG**. In 'sequential' mode, each protein will be digested by each enzyme, one by one. Launching 3 times **RPG** on the same protein with 3 different enzymes or launching one time **RPG** on the protein with the 3 enzymes in 'sequential' mode leads to exactly the same result.
+There are two digestion modes in **RPG**. In 'sequential' mode, each protein will be digested by each enzyme, one by one. Launching 3 times **RPG** on the same protein with 3 different enzymes or launching one time **RPG** on the protein with the 3 enzymes in 'sequential' mode leads to exactly the same result.
-In concurrent mode, all enzymes are present at the same time during digestion and exposure time is supposed to be infinite, i.e. all possible cleavages **will** occur (there is no miscleavage). In this mode, the cleavage of a first enzyme can make available the cleavage site of another enzyme.
+In concurrent mode, all enzymes are present at the same time during digestion and exposure time is supposed to be infinite, *i.e.* all possible cleavages **will** occur (there is no miscleavage). In this mode, the cleavage of a first enzyme can make available the cleavage site of another enzyme.
-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:
+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
@@ -202,7 +206,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
>Input_0_afterK_0_8_919.17848_11.27
PKPKPKPK
-'afterP' cleaves like expected and 'afterK' is not able to cleave anything.
+'afterP' cleaves as expected and 'afterK' is not able to cleave anything.
Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the following result:
@@ -228,15 +232,15 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow
Here, we have to understand that 'afterP' cleaves at the same positions as in sequential mode and the products (mostly 'KP') are then cleaved by 'afterK'. Indeed, there is no more P before K, making 'afterK' able to cleave.
-Default mode is 'sequential' and you can input miscleavage values only on this mode.
+Default mode is 'sequential'. Reminder: you can input miscleavage values only for this mode.
.. _misscleavage:
Miscleavage
-=============
+===========
-Sometimes, an enzyme does not cleave at a given position even if requirements are fulfilled. This event is called miscleavage and can have biological, chemical or physical origins. To take into account this behavior in **RPG**, one can assign a miscleavage value to an enzyme, expressed as a **percentage**.
+Sometimes an enzyme does not cleave at a given position even if requirements are fulfilled. This event is called miscleavage and can have biological, chemical or physical origins. To take into account this behavior in **RPG**, one can assign a miscleavage value to an enzyme, expressed as a **percentage**.
For example, using:
@@ -252,7 +256,7 @@ will assign a miscleavage probability of `1.4%` to enzyme `1`, a miscleavage pro
Non-interactive mode
====================
-Option **-n, --noninteractive** force **RPG** to not print any standard output, only error(s) are displayed in the shell. It enable '--quiet' option and overwrites --verbose option. If output filename already exists, output file will be systematically overwritten. This option is mostly used in cluster or pipeline when user does not want **RPG** to wait for input or display anything but errors.
+Option **-n, -\\-noninteractive** force **RPG** to not print any standard output, only error(s) are displayed in the shell. It enable '-\\-quiet' option and overwrites -\\-verbose option. If output filename already exists, the output file will be systematically overwritten. This option is mostly used in cluster or pipeline when user does not want **RPG** to wait for input or display anything but errors.
.. _formats:
@@ -260,22 +264,25 @@ Option **-n, --noninteractive** force **RPG** to not print any standard output,
Output
======
-Output of **RPG** contains several informations for each generated peptide, in this order:
+Output of **RPG** contains the following information in one line for each generated peptide, in this order:
- - Original header of original sequence
- - Number of this peptide for the original sequence
- - Enzyme used to obtain this peptide
+ - Header of original sequence or 'Input' if the sequence is directly inputed in **RPG**, *i.e.*, **-i** not used with a file
+ - Sequential numbering (starting from 0) of out-coming peptides for each of original sequence
+ - Enzyme name used to obtain this peptide
- Cleavage position on the original sequence (0 if no cleavage occurs)
- Peptide size
- Peptide molecular weight estimation
- Peptide isoelectric point estimation (pI)
+
+Then, on the next line:
+
- Peptide sequence
-Peptide molecular weight approximation is computed as the addition of average isotopic masses of each amino acid present in the peptide. Then the average isotopic mass of one water molecule is added to it. Molecular weight values are given in Dalton (Da). It does not take into consideration any kind of modification and for the first and last peptide.
+Peptide molecular weight approximation is computed as the addition of average isotopic masses of each amino acid present in the peptide. Then the average isotopic mass of one water molecule is added to it. Molecular weight values are given in Dalton (Da). It does not take into consideration any digestion-induced modifications.
-Isoelectric point is computed by solving Henderson–Hasselbalch equation using binary search. It is based on Lukasz P. Kozlowski works (http://isoelectric.org/index.html).
+The isoelectric point is computed by solving Henderson–Hasselbalch equation using binary search. It is based on Lukasz P. Kozlowski work (http://isoelectric.org/index.html).
-The default output is in multi fasta format. The header then summarize all those informations. For example, on the following fasta result:
+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
@@ -284,9 +291,9 @@ The default output is in multi fasta format. The header then summarize all those
>Input_1_Asp-N_8_5_742.78688_4.16
...
-we can see that a sequence was directly inputed in **RPG** (`Input`), the first peptide (`0`) was obtain with `Asp-N` and this enzyme cleaved after the `3`rd amino acid in the original sequence. The peptide has a size of `3` amino acid, a molecular weight estimated at `419.43738` Da and a theoretical isoelectric point of `5.54`. The full sequence is then written (`QWS`), and after, the header of the second peptide is outputted, etc.
+we can see that a sequence was directly inputed in **RPG** `(Input)`, the first peptide `(0)` was obtained with `Asp-N` and this enzyme cleaved after the `3rd` amino acid in the original sequence. The peptide has a size of `3` amino acids, a molecular weight estimated at `419.43738` Da and a theoretical isoelectric point of `5.54`. The full sequence is then written `(QWS)`. The output of the remaining peptides follows in the same format.
-More informations can be outputted using :ref:`verbose` option.
+More information can be outputted using :ref:`verbose` option.
.. _random:
@@ -294,7 +301,7 @@ More informations can be outputted using :ref:`verbose` option.
Random names
============
-Option **-r, --randomname** force **RPG** to use a random name for output file. When using it, **RPG** will not ask user output file name **nor location**. Output file will be create in the folder from which the software is used. This option is generally used for testing or automatic tasks.
+Option **-r, -\\-randomname** force **RPG** to use a random name for output file. When using it, **RPG** will not ask user output file name **nor location**. The output file will be created in the working directory. This option is generally used for testing or automatic tasks.
.. _verbose:
@@ -302,9 +309,9 @@ Option **-r, --randomname** force **RPG** to use a random name for output file.
Verbosity
=========
-Verbosity can be increased or decreased in the shell. Output file is not affected by **-v** or **-q** options.
+Verbosity can be increased or decreased. The output file is not affected by **-v** or **-q** options.
-With default level (no **-v** nor **-q** option), output is, as explain in :ref:`formats`:
+With default verbosity level (no **-v** nor **-q** option), the output is:
.. code-block:: none
@@ -316,7 +323,7 @@ With default level (no **-v** nor **-q** option), output is, as explain in :ref:
>Input_2_Asp-N_10_2_280.28048_3.6
DF
-Increasing verbosity by one, i.e. using **-v**, leads to add informations about used options. For example:
+Increasing verbosity by one, *i.e.* using **-v**, adds information about used options. For example:
.. code-block:: none
@@ -336,7 +343,7 @@ Increasing verbosity by one, i.e. using **-v**, leads to add informations about
>Input_2_Asp-N_10_2_280.28048_3.6
DF
-Increasing verbosity by two, i.e. using **-vv**, leads to also add statistics about each digested proteins. For example:
+Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about each of the digested proteins. For example:
.. code-block:: none
@@ -365,7 +372,7 @@ Increasing verbosity by two, i.e. using **-vv**, leads to also add statistics ab
>Input_2_Asp-N_10_2_280.28048_3.6
DF
-Decreasing verbosity, i.e. using **-q** option, remove all informations except errors. For example:
+Decreasing verbosity, *i.e.* using **-q** option, removes all information but errors. For example:
.. code-block:: none
@@ -380,9 +387,9 @@ Decreasing verbosity, i.e. using **-q** option, remove all informations except e
Creating a new enzyme
=====================
-Option **-a, --addenzyme** let the user to define new enzymes. An enzyme contains one or several rules and exceptions.
+Option **-a, -\\-addenzyme** allows the user to define new enzymes. An enzyme contains one or several rules and exceptions.
-On the following, nomenclature of `Schechter and Berger <https://www.ncbi.nlm.nih.gov/pubmed/6035483>`_ is used. According to it, 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 '|':
+On 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
@@ -398,7 +405,7 @@ In **RPG**, this nomenclature is represented as:
Definition of rules
-------------------
-A rule specify which amino acid is targeted by the enzyme, the cleavage position (i.e. **before** or **after** the targeted amino acid) and optionally the surrounding context. Each amino acid must be surrounded by parenthesis, i.e. '**(**' and '**)**' and the cleavage position is symbolized by a comma, i.e. '**,**'. The comma must always be directly before or after a parenthesis.
+A rule specifies which amino acid is targeted by the enzyme, the cleavage position (*i.e.* **before** or **after** the targeted amino acid) and optionally the surrounding context. Each amino acid must be included in parentheses, *i.e.* '**(**' and '**)**' and the cleavage position is represented by a comma, *i.e.* '**,**'. The comma must always be directly before or after an closing or opening parenthesis, respectively.
For example, to define a cleavage occurring **before** A, one must input:
@@ -412,14 +419,13 @@ To define a cleavage occurring **after** B, one must input:
(B,)
-The 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:
+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
(C)()(B)(,A)(D)
-Note that this enzyme will only cleave if it finds the motif C*BAD, where * is **one** amino acid, no matter which one.
-It will **not** cleave BAD, nor C*BA, BA, AD, etc. For example:
+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
@@ -435,25 +441,26 @@ It will **not** cleave BAD, nor C*BA, BA, AD, etc. For example:
Add an other enzyme? (y/n)
n
- $ rpg -i CWBADE -e 28
+ $ rpg -i CWBADE -e 43
>Input_0_rpg_example_userguide_3_3_307.36728_5.46
CWB
>Input_1_rpg_example_userguide_6_3_333.29818_3.4
ADE
- $ rpg -i FAD -e 28
+ $ rpg -i FAD -e 43
>Input_0_rpg_example_userguide_0_3_351.35928_3.6
FAD
-To make this enzyme always cleaves, for example, before A (`P1'`) followed by D in `P2'`, on top of the previous rule, one has to defined two rules in **RPG**:
+In order for this enzyme to also cleave before AD (before A `(P1')` followed by D in `P2'` ), on top of the previous rule, one has to define one more rule in **RPG**:
.. code-block:: none
(,A)(D)
(C)()(B)(,A)(D)
-Not that this enzyme will **not** cleave BAD, has 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*, has D is require in `P2'` for the second rule:
+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 the second rule.
+
.. code-block:: none
@@ -473,19 +480,19 @@ Not that this enzyme will **not** cleave BAD, has it is specified that it will c
Add an other enzyme? (y/n)
n
- $ rpg -i CWBADE -e 28
+ $ rpg -i CWBADE -e 43
>Input_0_rpg_example_userguide_3_3_307.36728_5.46
CWB
>Input_1_rpg_example_userguide_6_3_333.29818_3.4
ADE
- $ rpg -i FAD -e 28
+ $ rpg -i FAD -e 43
>Input_0_rpg_example_userguide_1_1_165.19188_5.54
F
>Input_1_rpg_example_userguide_3_2_204.18268_3.6
AD
- $ rpg -i BAD -e 28
+ $ rpg -i BAD -e 43
>Input_0_rpg_example_userguide_0_3_204.18268_3.6
BAD
@@ -535,13 +542,13 @@ Definition of exceptions
An exception specify when a cleavage should **not** occurs. **Exceptions must always be linked to a rule**.
-For example, to define a cleavage occurring **before** A (`P1'`), one must input:
+For example, to define a cleavage occurring **before** A `(P1')`, one must input:
.. code-block:: none
(,A)
-Exceptions can then be inputted, for example a cleavage occurs before A(`P1'`), except when P is in (`P2'`) is defined by adding this exception:
+Exceptions can then be inputted, for example a cleavage occurs before A in `P1'`, except when P is in `P2'` is defined by adding this exception:
.. code-block:: none
@@ -567,13 +574,13 @@ This enzyme will always cleave before A when not followed by P:
Add an other enzyme? (y/n)
n
- rpg -i CWBADE -e 28
+ rpg -i CWBADE -e 43
>Input_0_rpg_example_userguide_3_3_307.36728_5.46
CWB
>Input_1_rpg_example_userguide_6_3_333.29818_3.4
ADE
- rpg -i CWBAPE -e 28
+ rpg -i CWBAPE -e 43
>Input_0_rpg_example_userguide_0_6_604.67828_3.6
CWBAPE
@@ -607,21 +614,21 @@ This enzyme will always cleave before A when not followed by P or preceded by G
Add an other enzyme? (y/n)
n
- rpg -i CWBADE -e 28
+ rpg -i CWBADE -e 43
>Input_0_rpg_example_userguide_3_3_307.36728_5.46
CWB
>Input_1_rpg_example_userguide_6_3_333.29818_3.4
ADE
- rpg -i CWBAPE -e 28
+ rpg -i CWBAPE -e 43
>Input_0_rpg_example_userguide_0_6_604.67828_3.6
CWBAPE
- rpg -i GTBAPF -e 28
+ rpg -i GTBAPF -e 43
>Input_0_rpg_example_userguide_0_6_491.54438_5.54
GTBAPF
- rpg -i GTBAPE -e 28
+ rpg -i GTBAPE -e 43
>Input_0_rpg_example_userguide_3_3_176.17228_5.54
GTB
>Input_1_rpg_example_userguide_6_3_315.32628_3.6