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.