kraken-review

A Python 3.6+ library for analyzing Kraken output

Introduction · Tutorial · Installation

Introduction

This library demonstrations parsing the summary results from the taxonomic sequence classifier Kraken into a tree representation.

Features that may be implemented include:

• Bar plot or scatter plot integration showing the magnitude of sequences assigned to each node in the phylogenetic tree.
• Method for forcing all counts either up or down a linear branch to simplify sequence classification.
• Clade collapsing based on taxonomic assignment and phylogenetic order.

Tutorial

>>> from kraken_review import KrakenSummary
>>> summary = KrakenSummary('sample-report.txt')
>>> summary.newick
'(((Mus musculus musculus:1):1,(Rattus norvegicus albus:1):1,Homo sapiens:1),unclassified:1);'

>>> canvas, coords = summary.toytree.draw(
>>>     width=500,
>>>     height=175,
>>>     tip_labels_color=['red', 'black', 'black', 'black'],
>>>     # Make Carl Linnaeus proud and italicize those species names!
>>>     tip_labels=[f'<i>{l}</i>' for l in summary.toytree.get_tip_labels()])

Installation

❯ pip install git+git://github.com/clintval/kraken-review.git