Commit 2f03d329 authored by Nicolas  MAILLET's avatar Nicolas MAILLET
Browse files

change -i to -s in user guide when needed

parent 6e0f498b
Pipeline #10927 passed with stages
in 58 seconds
...@@ -115,6 +115,8 @@ To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and ...@@ -115,6 +115,8 @@ To perform sequential digestion of the sequence "QWSDORESDF" with enzymes 2 and
rpg -s QWSDORESDF -o output_file.fasta -e 2 5 rpg -s QWSDORESDF -o output_file.fasta -e 2 5
.. _onefile:
Sequential digestion of a (multi)fasta file Sequential digestion of a (multi)fasta file
""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""
...@@ -160,7 +162,9 @@ Here are all available options in **RPG**: ...@@ -160,7 +162,9 @@ 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. **-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 or a single protein sequence without commentary. See :ref:`oneseq` for example. **-i, -\\-inputdata**: Input file, in (multi)fasta / fastq format. See :ref:`onefile` for example.
**-s, -\\-sequence**: Input a single protein sequence without commentary. See :ref:`oneseq` for example.
**-l, -\\-list**: Display the list of available enzymes. **-l, -\\-list**: Display the list of available enzymes.
...@@ -268,7 +272,7 @@ Output ...@@ -268,7 +272,7 @@ Output
Output of **RPG** contains the following information in one line for each generated peptide, in this order: Output of **RPG** contains the following information in one line for each generated peptide, in this order:
- Header of original sequence or 'Input' if the sequence is directly inputed in **RPG**, *i.e.*, **-i** not used with a file - Header of original sequence or 'Input' if the sequence is directly inputed in **RPG**, *i.e.*, **-s**
- Sequential numbering (starting from 0) of out-coming peptides for each of original sequence - Sequential numbering (starting from 0) of out-coming peptides for each of original sequence
- Enzyme name used to obtain this peptide - Enzyme name used to obtain this peptide
- Cleavage position on the original sequence (0 if no cleavage occurs) - Cleavage position on the original sequence (0 if no cleavage occurs)
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