Commit b443a234 authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

Correct typo and add doc for -p option

parent 409509ee
Pipeline #9134 passed with stages
in 55 seconds
......@@ -170,6 +170,8 @@ Here are all available options in **RPG**:
**-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt).
**-p, -\\-pka**: Define pKa values. Either 'ipc' or 'stryer' (default: ipc). IPC values come from `IPC_peptide <http://isoelectric.org/theory.html>`_ and Stryer values from Biochemistry Stryer, 7th edition.
**-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.
**-q, -\\-quiet**: No standard output, only error(s).
......
......@@ -277,7 +277,7 @@ def main():
"overwritten.")
parser.add_argument("-p", "--pka", metavar="", choices=['ipc', 'stryer'],
default="ipc", help="Define pKa values. Either 'ipc' "
"or 'stryer (default: ipc)")
"or 'stryer' (default: ipc)")
group_output = parser.add_mutually_exclusive_group()
group_output.add_argument("-o", "--outputfile", type=str, metavar="",
default="", help="Optional result file "
......
......@@ -84,7 +84,7 @@ AA_PKA_IPC = {"Nterm" : 9.564,
"R" : 12.503,
"Y" : 10.071,
"Cterm" : 2.383}
"""pKa of important amino acid to compute pI (from IPC)."""
"""pKa of important amino acid to compute pI (from IPC_peptide. See http://isoelectric.org/theory.html for details)."""
def handle_errors(message="", err=1, error_type=""):
"""Custom handling of errors and warnings.
......
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