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Classify C. Liberibacter solanacearum haplotypes

Project description

Documentation Status

Haplotype-LSO

Haplotype assignment of Candidatus Liberibacter solanacearum following IPPC (International Plant Protection Convention) standard DP 21: Candidatus Liberibacter solanacearum.

Quick Facts

  • License: MIT
  • Programming Language Python

Input / Output - What it Does!

This program takes as the input Sanger sequences from the 16S, 16S-23S, and 50S primers from the IPPC standard DP21. It then aligns them to the GenBank reference sequences EU812559 and EU834131 (as specified in DP21). Based on the alignments and the document DP21, sequence identity is computed and haplotyping is performed, yielding:

  • sequence identity to EU822559 for identifying the species C. Liberibacter solanacearum, and
  • haplotyping of the read based on variation from the reference sequence.

Sample names can be inferred from the read names or from a separate mapping TSV file.

Quick Start

This is gonna be really quick!

Installation

We recommend using Bioconda.

First install Bioconda. Then (clsify is the old package name of Haplotype-Lso and it will be renamed soon):

# conda install -y clsify

And – tadaa – you’re ready to go!

Running

You can have one FASTA (or FASTQ) file with all of your reads or one file for each. If you have a single sequence per FASTA (or FASTQ) file then you can use the file name instead of the sequence name.

# hlso -o result.tsv INPUT.fasta
## OR
# hlso [--use-file-name] -o result.tsv INPUT1.fasta INPUT2.fasta [...]
## e.g.,
# hlso [--use-file-name] -o result.tsv INPUT*.fasta

Developer Guide

Releasing Packages

For the PyPi package:

$ python setup.py sdist
$ twine upload --repository-url https://test.pypi.org/legacy/ dist/hlso-*.tar.gz
$ twine upload dist/hlso-*.tar.gz

For the Bioconda package, see the great documentation. The Docker image will automatically be created as a BioContainer when the Bioconda package is built.

History

v0.4.3

  • Fixing issue with AB1/SCF support.

v0.4.2

  • Fix for multi-region sequences.
  • Fixing collision, variant must be identified by sequence, position, and reference.

v0.4.1

  • Fixing bug with display of BLAST match.
  • Adding link-out to NCBI WWWBLAST submission.
  • Removing some cruft from repository.
  • Fixing bug in phylogenetic coputation in case of BLAST all-to-all matches not a square number.

v0.4.0

  • Compute region-wise phylogenetic tree.

v0.3.4

  • Support for uploading to PyPi.

v0.3.3

  • Fixing regular expression.

v0.3.2

  • Changing file name pattern do dot-separated scheme.
  • Greatly extending documentation.

v0.3.1

  • Starting out with tutorial and manual.

v0.3.0

  • Adding tutorial.
  • Rebranding as “Haplotype-LSO” (hlso).
  • Properly normalizing indels according to Tan et al. (2015).
  • Adding support for haplotyping with indels.

v0.2.0

  • Removing dependency on bcftools. Haplotyping is done from BLAST match now.
  • Adding tests for blast module.
  • Rewrite of the whole BLAST and haplotyping interface and architecture.

v0.1.1

  • Zapping gremlins in haplotype table.
  • Change formatting of README.

v0.1.0

Initial release.

  • Everything is new!

Project details


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