Metagenomix

Metagenomix is a tool which enables you to download, analyze and visualize metagenomic data.

Installation

Clone this repository and change to its directory. Then run:

# Download and setup NCBI taxonomy tree
./setup-tax
# Download and setup NCBI assembly summaries
./setup-ncbi
# Install the meta package
python setup.py build install

After the installation you should have available the python package meta.

Features

Taxonomy Tree

Metagenomix provides a tree-like structure for browsing taxonomy. Taxonomy is inferred from the taxdmp.zip downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/. Using taxonomy tree, you can easily explore the NCBI taxonomy. For instance,

from meta.data.tax import TaxTree

tt = TaxTree() # takes some time to load taxonomy
tt.get_org_name(83333) # 83333 is taxid of Escherichia coli K-12
tt.get_org_rank(83333) # has no rank assignment
tt.get_parent_with_rank(83333, 'species') # we find the species parent of this strain, returns 562
tt.get_org_name(562) # returns Escherichia coli
# Test if 83333 is child of 562
tt.is_child(83333, 562)	# returns True
# Let's find the Least Common Ancestor (LCA) of Escherichia coli and Bacillus subtilis
tt.get_org_name(tt.find_lca((1423, 562))) # returns Bacteria

NCBI download with taxonomy filtering

Using the meta package, you can download genome data from NCBI (using refseq or genbank). This can be done in two ways. First is to specify for which species or species subtree (including species children) you want to download genome data, by using the ncbi-download tax tool. If we want to download all the Escherichia coli (taxid: 562) subspecies from RefSeq and extract the genome files while downloading, we envoke:

ncbi-download tax refseq 562 ./output_dir --children --extract

If you, however, want a custom list of genomes, there is a database at your disposal, creating by parsing the assembly_summary_{genbank/refseq}.txt files, in the meta/data/NCBI.db file. It is a sqlite3 database, and can be acessed (for instance) by using a Firefox plugin: https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager/. Here you can formulate any queries on the database, and put the resulting list of ftp_paths in a file, and invoke:

ncbi-download url url_list_file.txt ./output_dir

The MIT Licence

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.