README.md

bacteria_genome_pull

Download latest bacterial sequencing assembly files from NCBI database (RefSeq or Genbank)

To access help menu:

python bacteria_genome_pull.py or python bacteria_genome_pull.py -h

Basic Usage:

python bacteria_genome_pull.py -b Klebsiella_pneumoniae

This will download all latest assembly sequencing files in fna format for Klebsiella pneumoniae from refseq. All files will be downloaded to current directory.

Change NCBI database:

python bacteria_genome_pull.py -d genbank -b Klebsiella_pneumoniae

If no -d argument is given, will default to refseq

Change file type:

python bacteria_genome_pull.py -t gff -b Klebsiella_pneumoniae

This will download the gff file for all Klbesiella pneumoniae genomes in refseq

If no -t argument is given, will default to fna

Which genomes are available:

python bacteria_genome_pull.py -g refseq

This will provide a list of all available bacterial genomes in refseq

Specify output directory:

python bacteria_genome_pull.py -b Klebsiella_pneumoniae -o path/to/foo

Will output all fna files to foo directory.

This will create foo directory if it does not exist.

Argument Options:

Argument	Explanation	Option(s)
-b (required)	bacterium	name of bacterium
-t (optional)	file type	fna (default)
		gbb
		genbank
		feature_table
-d (optional)	database	refseq (default)
		genbank
-g (optional)	available genomes	refseq (default)
		genbank
-o (optional)	output directory	. (defualt)

Examples

Download all refseq bacterial genomes (in fna format)

python bacteria_genome_pull.py -b *

Download all Klebsiella genbank files from refseq

python bacteria_genome_pull.py -t genbank -b Klebsiella*

Download all Klebsiella pneumoniae gff files from genbank and store in foo directory

python bacteria_genome.py -t gff -d genbank -o directory -b Klebsiella_pneumoniae