rpg -i input_file.fasta -o output_file.fasta -e 2 5 -d c
Adding a new enzyme
-------------------
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@@ -156,7 +156,7 @@ Here are all available options in **RPG**:
**-d, -\\-digest**: Digestion mode. Either 's', 'sequential', 'c' or 'concurrent' (default: s). See :ref:`digestion` for more information.
**-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.
**-e, -\\-enzymes**: Enzyme(s) id number to use (*i.e.* -e 0 5 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 information.
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@@ -164,7 +164,7 @@ Here are all available options in **RPG**:
**-l, -\\-list**: Display the list of available enzymes.
**-m, -\\-miscleavage**: 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:`miscleavage` for more information.
**-m, -\\-miscleavage**: 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 5.2 10). It works only for sequential digestion (default: 0). See :ref:`miscleavage` 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 information.
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@@ -192,7 +192,7 @@ Let's define two enzymes. The first is called 'afterP' (id 28) and cleaves after
.. code-block:: none
$ rpg -i PKPKPKPK -e 28 -e 29
$ rpg -i PKPKPKPK -e 28 29
>Input_0_afterP_1_1_115.13198_5.54
P
>Input_1_afterP_3_2_243.30608_9.4
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@@ -212,7 +212,7 @@ Digesting 'PKPKPKPK' using those two enzymes in concurrent mode gives the follow
.. code-block:: none
$ rpg -i PKPKPKPK -e 28 -e 29 -d c
$ rpg -i 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
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@@ -246,7 +246,7 @@ For example, using:
.. code-block:: none
rpg -i QWSDORESDF -e 1 -e 2 -e 3 -m 1.4 -m 2.6
rpg -i 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.