diff --git a/docs/userguide.rst b/docs/userguide.rst index 412b28a6be2617936c1142d851ab94033074774d..bd3785944d2947bc956d46c5d9efb854c46bebfa 100644 --- a/docs/userguide.rst +++ b/docs/userguide.rst @@ -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 +.. _onefile: + Sequential digestion of a (multi)fasta file """"""""""""""""""""""""""""""""""""""""""" @@ -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. -**-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. @@ -268,7 +272,7 @@ Output 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 - Enzyme name used to obtain this peptide - Cleavage position on the original sequence (0 if no cleavage occurs)