Package: aakbar
Amino-Acid k-mer tools for creating, searching, and analyzing phylogenetic signatures from genomes or reads of DNA.PrerequisitesA 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 thepyfastaq  https://pypi.python.org/pypi/pyfastaqpackage.If you don’t have a python installed that meets these requirements, I recommend gettingAnaconda 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 pyfastaqInstallationThis 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 aakbarIf you wish to develop aakbar,  download areleaseand 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.gitUsageInstallation puts a single script calledaakbarin your path.  The usage format is:aakbar [GLOBALOPTIONS] COMMAND [COMMANDOPTIONS] [ARGS]A listing of commands is available viaaakbar--help.  Current available commands are:calculate-peptide-termsWrite peptide terms and histograms.conserved-signature-statsStats on signatures found in all input genomes.define-setDefine an identifier and directory for a set.define-summaryDefine summary directory and label.demo-simplicityDemo self-provided simplicity outputs.filter-peptide-termsRemove high-simplicity terms.init-config-fileInitialize a configuration file.install-demo-scriptsCopy demo scripts to the current directory.intersect-peptide-termsFind intersecting terms from multiple sets.label-setDefine label associated with a set.peptide-simplicity-maskLower-case high-simplicity regions in FASTA.search-peptide-occurrancesFind signatures in peptide space.set-simplicity-windowDefine size of window used in simplicity calcs.set-plot-typeDefine label associated with a set.set-simplicity-typeSelect function used in simplicity calculation.show-configPrint location and contents of config file.show-context-objectPrint the global context object.test-loggingLogs at different severity levels.ExamplesBash 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-scriptsOn linux and MacOS, follow the instructions to run the demos.  On Windows, you will
needbashinstalled for the scripts to work.ToolsIn addition to pyfastaq, two tools that you will probably find helpful in working
with aakbar arealphabetsoup <https://github.com/ncgr/alphabetsoup>for sanitizing input FASTA files andtsv-tools <https://https://github.com/eBay/tsv-utils/>for filtering
output TSV files.Latest ReleaseGitHubLicenseDocumentationTravis BuildCoverageCode GradeDependenciesIssues