安装
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| mamba create -n magpurify2
mamba activate magpurify2
pip install magpurify2
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数据库下载
数据库存放在谷歌云盘上，有15G，我选择临时租个阿里云新加坡的服务器下载了再传回来。
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| fileId="1ooWiR3LplBy5GsY5wZ7o6dwswiCWVvmi"
fileName="magpurify2DB.v1.0.tar.gz"
curl -sc /tmp/cookie "https://drive.google.com/uc?export=download&id=${fileId}" > /dev/null
code="$(awk '/_warning_/ {print $NF}' /tmp/cookie)"
curl -Lb /tmp/cookie "https://drive.google.com/uc?export=download&confirm=${code}&id=${fileId}" -o ${fileName}
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传输完成后解压即可。
运行
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| magpurify2 taxonomy -t 60 final_assembly.fasta mapurify2.taxonomy ~/database/magpurify2
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结果：
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| genome contig genome_taxonomy contig_taxonomy
final_assembly k141_419989 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae
final_assembly k141_296469 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Gammaproteobacteria;Xanthomonadales;Xanthomonadaceae
final_assembly k141_160589 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Rhizobiaceae;Allorhizobium
final_assembly k141_432342 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Alphaproteobacteria;Sphingomonadales;Sphingomonadaceae;Sphingopyxis
final_assembly k141_716437 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Gammaproteobacteria;Burkholderiales;Burkholderiaceae;Acidovorax_E
final_assembly k141_580566 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Enterobacteriaceae;Enterobacter
final_assembly k141_24707 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Gammaproteobacteria;Burkholderiales;Burkholderiaceae
final_assembly k141_12355 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Flavobacteriaceae;Flavobacterium
final_assembly k141_370583 root;Bacteria;Proteobacteria;Gammaproteobacteria root;Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae
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