protein_annotator

protein_annotator

This tool adds a protein accession column to a text file based on the present peptides.

The column containing the peptide string must be defined. Then, all proteins that match the given peptide are written to a specified column.

Usage:

protein_annotator.py –input=<input.tsv> –output=<extended_file.tsv> –fasta=<fasta_file.fasta>

[–peptide_column=<column_name>] [–protein_column=<column_name>] [–protein_separator=<separator>] [–column_separator=<separator>] [–ignore_il]

protein_annotator.py (–help | –version)

Options:

-i, --input=<input.tsv>
	Path to the input file.
-o, --output=<extended_file.tsv>
	Path to the output file that should be created.
-f, --fasta=<fasta_file.fasta>
	Fasta file to match the peptides to.
--peptide_column=<column_name>
	Column name of the peptide column [default: sequence]
--protein_column=<column_name>
	Column name of the newly added protein column [default: protein]
--protein_separator=<separator>
	Separator to separate multiple protein entries [default: ;]
--column_separator=<separator>
	Separator to separate columns in the file [default: TAB]
--ignore_il	If set I/L are treated as synonymous.
-h, --help	Print this help message.
-v, --version	Print the current version.