Hierarchical taxonomic classifier
Project description
HiTaC
A hierarchical taxonomic classifier for fungal ITS sequences.
Installation
HiTaC dependends on QIIME 2. We recommend using QIIME 2 version 2020.2. To install QIIME 2 in a new conda environment and activate it, please run:
wget https://data.qiime2.org/distro/core/qiime2-2020.2-py36-linux-conda.yml
conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml
conda activate qiime2-2020.2
Afterwards, HiTaC can be installed using either conda or pip:
conda install hitac
pip install hitac
Input Files
HiTaC accepts taxonomy in TSV format and training and test files in FASTA format. All these files must be previously imported by QIIME 2. For example:
qiime tools import \
--input-path $qfa \
--output-path q-seqs.qza \
--type 'FeatureData[Sequence]'
qiime tools import \
--input-path dbq.fa \
--output-path db-seqs.qza \
--type 'FeatureData[Sequence]'
qiime tools import \
--type 'FeatureData[Taxonomy]' \
--input-format HeaderlessTSVTaxonomyFormat \
--input-path db-tax.txt \
--output-path db-tax.qza
To train the model and classify, simply run:
qiime hitac classify \
--i-reference-reads db-seqs.qza \
--i-reference-taxonomy db-tax.qza \
--i-query q-seqs.qza \
--o-classification classifier_output.qza --verbose
Running
To see the usage run qiime hitac --help
Usage: qiime hitac [OPTIONS] COMMAND [ARGS]...
Description: This QIIME 2 plugin wraps HiTaC and supports hierarchical
taxonomic classification.
Plugin website: https://gitlab.com/dacs-hpi/hitac
Getting user support: Please post to the QIIME 2 forum for help with this
plugin: https://forum.qiime2.org
Options:
--version Show the version and exit.
--citations Show citations and exit.
--help Show this message and exit.
Commands:
classify HiTaC
Output File
The predictions can be exported from QIIME 2 to a TSV file:
qiime tools export \
--input-path classifier_output.qza \
--output-path output_dir
The first column in the TSV file contains the identifier of the test sequence and the second column holds the predictions made by HiTaC. For example:
Feature ID Taxon Confidence
EU254776;tax=d:Fungi,p:Ascomycota,c:Sordariomycetes,o:Diaporthales,f:Gnomoniaceae,g:Gnomonia; d__Fungi; p__Ascomycota; c__Sordariomycetes; o__Diaporthales; f__Valsaceae; g__Cryptosporella -1
FJ711636;tax=d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Agaricales,f:Marasmiaceae,g:Armillaria; d__Fungi; p__Basidiomycota; c__Agaricomycetes; o__Agaricales; f__Marasmiaceae; g__Armillaria -1
UDB016040;tax=d:Fungi,p:Basidiomycota,c:Agaricomycetes,o:Russulales,f:Russulaceae,g:Russula; d__Fungi; p__Basidiomycota; c__Agaricomycetes; o__Russulales; f__Russulaceae; g__Russula -1
GU827310;tax=d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Ramalinaceae,g:Ramalina; d__Fungi; p__Ascomycota; c__Lecanoromycetes; o__Lecanorales; f__Ramalinaceae; g__Ramalina -1
JN943699;tax=d:Fungi,p:Ascomycota,c:Lecanoromycetes,o:Lecanorales,f:Parmeliaceae,g:Melanohalea; d__Fungi; p__Ascomycota; c__Lecanoromycetes; o__Lecanorales; f__Parmeliaceae; g__Punctelia -1
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