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Distribution-based OTU calling

Project description

dbotu3 is a new implementation of Sarah Preheim’s dbOTU algorithm. The scope is narrower, the numerical comparisons are faster, and the interface is more user-friendly.

Read the documentation for:

  • a guide to getting started,

  • an explanation of the algorithm, and

  • the API reference.

You can also read our new paper for more technical details about the algorithm. The Alm Lab website also has a short page with information.

Installation

dbotu3 is on PyPi and can be installed with pip.

Requirements

Version history

  • 1.1: Corrected error where sequence IDs that could be read as integers would not be found in the table

  • 1.2: Python 2 compatibility, tox test framework, warnings for improperly-formatted sequence count tables

  • 1.2.1: Added setup requirements

  • 1.3.0: Improved OTU file header. Split the log file into a debug and progress log.

  • 1.4.0: Made an improvement to the Levenshtein-based genetic dissimilarity metric.

To-do

  • Fix the output format (maybe put OTU_ID in the first field and row?)

  • Find a way to avoid reading the entire count file? (The fasta file is not all loaded because we use SeqIO.index.)

  • Better coverage for unit tests

Author

Scott Olesen / swo at alum.mit.edu

Project details


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Source Distribution

dbotu-1.4.0.tar.gz (9.1 kB view hashes)

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