@@ -194,7 +194,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
.. code-block:: none
$ rpg -i PKPKPKPK -e 28 29
$ rpg -s PKPKPKPK -e 28 29
>Input_0_afterP_1_1_115.13198_5.54
P
>Input_1_afterP_3_2_243.30608_9.4
...
...
@@ -214,7 +214,7 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow
.. code-block:: none
$ rpg -i PKPKPKPK -e 28 29 -d c
$ rpg -s PKPKPKPK -e 28 29 -d c
>Input_0_afterP-afterK_1_1_115.13198_5.54
P
>Input_1_afterP-afterK_2_1_146.18938_9.4
...
...
@@ -248,7 +248,7 @@ For example, using:
.. code-block:: none
rpg -i QWSDORESDF -e 1 2 3 -m 1.4 2.6
rpg -s QWSDORESDF -e 1 2 3 -m 1.4 2.6
will assign a miscleavage probability of `1.4%` to enzyme `1`, a miscleavage probability of `2.6%` to enzyme `2` and a miscleavage probability of `0%` to enzyme `3` (default behavior). For enzyme `1`, each cleavage will then have a probability of 0.014 to **not** occur.
...
...
@@ -317,7 +317,7 @@ With default verbosity level (no **-v** nor **-q** option), the output is:
.. code-block:: none
$ rpg -i QWSDORESDF -e 1
$ rpg -s QWSDORESDF -e 1
>Input_0_Asp-N_3_3_419.43738_5.54
QWS
>Input_1_Asp-N_8_5_742.78688_4.16
...
...
@@ -329,7 +329,7 @@ Increasing verbosity by one, *i.e.* using **-v**, adds information about used op
.. code-block:: none
$ rpg -i QWSDORESDF -e 1 -v
$ rpg -s QWSDORESDF -e 1 -v
Warning: File 'peptides.fasta' already exit!
Overwrite it? (y/n)
y
...
...
@@ -349,7 +349,7 @@ Increasing verbosity by two, *i.e.* using **-vv**, also adds statistics about ea
.. code-block:: none
$ rpg -i QWSDORESDF -e 1 -vv
$ rpg -s QWSDORESDF -e 1 -vv
Warning: File 'peptides.fasta' already exit!
Overwrite it? (y/n)
y
...
...
@@ -378,7 +378,7 @@ Decreasing verbosity, *i.e.* using **-q** option, removes all information but er
.. code-block:: none
$ rpg -i QWSDORESDF -e 1 -q
$ rpg -s QWSDORESDF -e 1 -q
Warning: File 'peptides.fasta' already exit!
Overwrite it? (y/n)
y
...
...
@@ -443,13 +443,13 @@ Note that this enzyme will only cleave if it finds the motif C*BAD, where * coul
Add another enzyme? (y/n)
n
$ rpg -i CWBADE -e 43
$ rpg -s 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 43
$ rpg -s FAD -e 43
>Input_0_rpg_example_userguide_0_3_351.35928_3.6
FAD
...
...
@@ -482,19 +482,19 @@ It is important to note that for each enzyme, it is enough that one of the rule
Add another enzyme? (y/n)
n
$ rpg -i CWBADE -e 43
$ rpg -s 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 43
$ rpg -s 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 43
$ rpg -s BAD -e 43
>Input_0_rpg_example_userguide_0_3_204.18268_3.6
BAD
...
...
@@ -576,13 +576,13 @@ This enzyme will always cleave before A when not followed by P:
Add another enzyme? (y/n)
n
rpg -i CWBADE -e 43
rpg -s 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 43
rpg -s CWBAPE -e 43
>Input_0_rpg_example_userguide_0_6_604.67828_3.6
CWBAPE
...
...
@@ -616,25 +616,25 @@ This enzyme will always cleave before A (`P1'` ) when not followed by P (`P2'` )
