这个需求的起因就是因为 QIIME 自带 plot_taxa_summary.py 脚本生成的图表太难看, 所以就着手处理了一下
本来是想在biostar上面找现成的轮子, 结果没找到, 只有自己做了.
附上在biostar.org上的回答内容
Hi, hope this answer is not too late. :)
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| biom convert -i single_sample.biom -o single_sample.tsv --to-tsv --table-type "OTU table" --header-key taxonomy
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| # take a look at single_sample.tsv
$ head single_sample.tsv
# Constructed from biom file
#OTU ID H2O taxonomy
346085 140.0 Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas; Brevundimonas_bullata
10298 2.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus; Photorhabdus_temperata
122823 3.0 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Massilia; EF516371_s
130468 2.0 Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Sphingomonadaceae; Sphingopyxis; Sphingopyxis_witflariensis
139977 38.0 Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Erythrobacter; Erythrobacter_flavus
121751 2.0 Bacteria; Firmicutes; Clostridia; Clostridiales; Lachnospiraceae; Catonella; JX096343_s
96934 10.0 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas; Pseudomonas_guguanensis
95181 4.0 Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales; Moraxellaceae; Acinetobacter; Acinetobacter_radioresistens
# remove the comments
$ egrep -v "^#" single_sample.tsv > sample_no_comment.tsv
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remove the first column
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| $ cut sample_no_comment.tsv -f 2- > sample.tsv
$ head -n2 sample.tsv
140.0 Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales; Caulobacteraceae; Brevundimonas; Brevundimonas_bullata
2.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Photorhabdus; Photorhabdus_temperata
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replace the "; " with "\t"
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| $ sed -i 's/;\s*/\t/g' sample.tsv
$ head -n2 sample.tsv
140.0 Bacteria Proteobacteria Alphaproteobacteria Caulobacterales Caulobacteraceae Brevundimonas Brevundimonas_bullata
2.0 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Photorhabdus Photorhabdus_temperata
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now we can make a pie chart with ktImportText(One of the Krona tools)
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| $ ktImportText -n enjoy_your_life -o sample.krona.html sample.tsv
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open sample.krona.html with your web browser, you'll see this
all in one command(optional)
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| $ awk -F '\t|;' 'BEGIN{OFS="\t"} FNR > 2 {$1=""; print $0}' single_sample.tsv | cut -f 2- > sample.tsv
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