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). If a directory, file name is prepended to the label of each translated peptide originally coming from that file (i.e., to track the genome of origin) |
-x |
--prepend-filename |
whether to prepend file name to peptide sequences when a directory with multiple fasta or genbank files is used as input. | |
-o |
--outfile |
None |
path to output (labelled peptide database) file. Defaults to file in directory of input data. |
-p |
--processes |
None |
set maximum number of processes. Defaults to all but one. |
-t |
--tempdir |
None |
path to directory to store temporary files. Defaults to system temp directory. |
-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.