等级分类法
hitac的Python项目详细描述
希塔克
真菌ITS序列的层次分类分类器。在
安装
希塔克依靠奇美2号。我们建议使用QIIME2020.2版。要安装它并激活新环境,请运行:
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
安装了QIIME 2后,可以使用conda或pip安装HiTaC:
^{pr2}$跑步
查看用法运行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
输入文件
HiTaC接受TSV格式的分类法和FASTA格式的培训和测试文件。所有这些文件必须由qiime2预先导入。例如:
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
要训练模型并进行分类,只需运行:
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
输出文件
预测可以从QIIME 2导出到TSV文件:
qiime tools export \
--input-path classifier_output.qza \
--output-path output_dir
TSV文件中的第一列包含测试序列的标识符,第二列包含HiTaC的预测。例如:
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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