diff --git a/docs/userguide.rst b/docs/userguide.rst index c3a57d384af085376d9ab0ba402ec0b0ba8fe202..9bd5640d510d0c5af328ee9d4b1f33566cc9ffa8 100644 --- a/docs/userguide.rst +++ b/docs/userguide.rst @@ -156,9 +156,11 @@ Here are all available options in **RPG**: **-a, -\\-addenzyme**: Add a new user-defined enzyme. See :ref:`addenzyme` for more information. +**-b, -\\-delenzyme**: Delete a user-define enzyme. See :ref:`delenzyme` for more information. + **-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 5 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 or name to use (*e.g.* -e 1 Asp-N 10 to use enzymes 1, Asp-N 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. @@ -168,14 +170,22 @@ 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 5.2 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 (*e.g.* -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. +**-x, -\\-cleave**: Cleavage site(s) when adding enzyme in non-interactive mode (*e.g.* -x "(D or E,)", similar to -x "(D,)" "(E,)". See :ref:`addenzyme` for more information. + +**-z, --exception**: Exception(s) when adding enzyme in non-interactive mode (*e.g.* -z "(D,)(W)" "(D,)(A)". See :ref:`addenzyme` for more information. + +**-y, --enzname**: Enzyme's name when adding enzyme in non-interactive mode. See :ref:`addenzyme` for more information. + **-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt). **-p, -\\-pka**: Define pKa values. Either 'ipc2', 'stryer' or 'ipc' (default: ipc2). IPC2 values come from `IPC_peptide in Supplementary Table S1 <https://doi.org/10.1093/nar/gkab295>`_, Stryer values from Biochemistry Stryer, 7th edition and IPC values from `IPC_peptide <http://isoelectric.org/theory.html>`_. +**-w, --mass**: Define atomic mass values. Either 'avg' for average mass or 'mono' for monoisotopic mass. + **-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information. **-c , -\\-processes**: Number of parallel processes to use (default: 1) @@ -761,7 +771,13 @@ Example of enzymes All available enzymes are in :ref:`enzymes`, including their **RPG**'s definition. +Non-interactive mode +-------------------- + +Using **-n, -\\-noninteractive** and **-a, -\\-addenzyme** options together is possible, but then requires to also use **-x, -\\-cleave** option to define cleaving site(s), **-y, --enzname** option to define the name of the enzyme and optionally **-z, --exception** option to define exceptions. + +.. _delenzyme: Deleting user-defined enzymes ============================= @@ -782,8 +798,8 @@ and finishes with: followed by 3 blank line. -To remove an enzyme, be sure to backup the file **before** any modifications. Then just remove the whole Python code of the enzyme, including the above-mentioned lines. Do not do any other modifications, as this code is used in **RPG** and any wrong modifications will make the software unable to run. +To remove an enzyme, use the option **-b, -\\-delenzyme** with the id or name of the user-defined enzyme to remove. It is not possible to remove predefined enzymes of **RPG**. To remove all user-defined enzymes, just delete ``~/rpg_user.py`` file. It will be created again (empty) at the next launch of **RPG**. -Obviously, all deleted enzymes can not be recovered. If one wants to use them again they will need to be redefined in **RPG**, using -a option. \ No newline at end of file +Obviously, all deleted enzymes can not be recovered. If one wants to use them again they will need to be redefined in **RPG**, using **-a, -\\-addenzyme** option.