Commit cf7d469b authored by Nicolas  MAILLET's avatar Nicolas MAILLET
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Update doc for gzipped and parallel

parent 8399ce9a
......@@ -29,7 +29,7 @@ Overview
Rapid Peptides Generator (RPG), is a standalone software dedicated to predict proteases-induced cleavage sites on sequences.
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.
RPG is a python tool taking a (multi-)fasta/fastq file (gzipped or not) 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.
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......@@ -162,7 +162,7 @@ Here are all available options in **RPG**:
**-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. See :ref:`onefile` for example.
**-i, -\\-inputdata**: Input file, in (multi)fasta / fastq format (gzipped or not). See :ref:`onefile` for example.
**-s, -\\-sequence**: Input a single protein sequence without commentary. See :ref:`oneseq` for example.
......@@ -178,6 +178,8 @@ Here are all available options in **RPG**:
**-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.
**-c , -\\-processes**: Number of parallel processes to use (default: 1)
**-q, -\\-quiet**: No standard output, only error(s).
**-v, -\\-verbose**: Increase output verbosity. -vv will increased more than -v. See :ref:`verbose` for more information.
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