build - Robaina/Pynteny Wiki

Translate assembly sequence data and assign positional metadata to labels

Usage

usage: pynteny build [-h] [args] 

Arguments

short long default help
-h --help show this help message and exit
-i --data None path to assembly input nucleotide data or annotated GenBank file. It can be a single file or a directory of files (either of FASTA or GeneBank format).
-o --outfile None path to output (labeled peptide database) file. Defaults to file in the directory of input data.
-n --processes None set the maximum number of processes. Defaults to all but one.
-l --log None path to log file. Log not written by default.

Description

Translate nucleotide assembly file and assign contig and gene location info to each identified ORF (using prodigal). Label predicted ORFs according to positional info and export a fasta file containing predicted and translated ORFs. Alternatively, extract peptide sequences from GenBank file containing ORF annotations and write labeled peptide sequences to a fasta file.