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aakbar 0.7.4

Amino-Acid k-mer Phylogenetic Signature Tools

Amino-Acid k-mer tools for creating, searching, and analyzing phylogenetic signatures from genomes or reads of DNA.

Prerequisites

A 64-bit Python 3.4 or greater is required. 8 GB or more of memory is recommended.

The python dependencies of aakbar are: biopython, click>=5.0, click_plugins numpy, pandas, pyfaidx, and pyyaml. Running the examples also requires the pyfastaq https://pypi.python.org/pypi/pyfastaq package.

If you don’t have a python installed that meets these requirements, I recommend getting Anaconda Python <https://www.continuum.io/downloads> on MacOSX and Windows for the smoothness of installation and for the packages that come pre-installed. Once Anaconda python is installed, you can get the dependencies like this on MacOSX:

export PATH=~/anaconda/bin:${PATH}    # you might want to put this in your .profile
conda install click
conda install --channel https://conda.anaconda.org/IOOS click-plugins
conda install --channel https://conda.anaconda.org/bioconda pyfaidx
conda install --channel https://conda.anaconda.org/bioconda pyfastaq  # only required for examples

Installation

This package is tested under Linux and MacOS using Python 3.5 and is available from the PyPI. To install via pip (or pip3 under some distributions) :

pip install aakbar

If you wish to develop aakbar, download a release and in the top-level directory:

pip install --editable .

If you wish to have pip install directly from git, use this command:

pip install git+https://github.com/ncgr/aakbar.git

Usage

Installation puts a single script called aakbar in your path. The usage format is:

aakbar [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS] [ARGS]

A listing of commands is available via aakbar --help. Current available commands are:

calculate_peptide_terms Write peptide terms and histograms.
conserved_signature_stats Stats on signatures found in all input genomes.
define_set Define an identifier and directory for a set.
define_summary Define summary directory and label.
demo_simplicity Demo self-provided simplicity outputs.
filter_peptide_terms Remove high-simplicity terms.
init_config_file Initialize a configuration file.
install_demo_scripts Copy demo scripts to the current directory.
intersect_peptide_terms Find intersecting terms from multiple sets.
label_set Define label associated with a set.
peptide_simplicity_mask Lower-case high-simplicity regions in FASTA.
search_peptide_occurrances Find signatures in peptide space.
set_letterfreq_window Define size of letterfreq window.
set_plot_type Define label associated with a set.
set_simplicity_object Select simplicity-calculation object.
show_config Print location and contents of config file.
show_context_object Print the global context object.
test_logging Logs at different severity levels.

Examples

Bash scripts that implement examples for calculating and using signature sets for Firmicutes and Streptococcus, complete with downloading data from GenBank, will be created in the (empty) current working directory when you issue the command:

aakbar install_demo_files

On linux and MacOS, follow the instructions to run the demos. On Windows, you will need bash installed for the scripts to work.

License

aakbar is distributed under a BSD License.

 
File Type Py Version Uploaded on Size
aakbar-0.7.4.tar.gz (md5) Source 2017-10-05 34KB