新技能Get!宏基因组分析结果导入qiime2分析和可视化

# qiime2使用，先转换成biom格式，界门纲目科属种间是以|分隔的，要替换成;，还有就是要去除属以上的级别，只保留种就可以了，qiime2会自动合并，否则导入不识别。
cp output_data/metaphlan/merged/metaphlan_taxonomic_profiles.tsv .
# qiime2认的表头有点死，改成它认的
cat meta.txt | cut -f 1 |sed  's/|/;/g' |less >tax_temp.txt
cat meta.txt | cut -f 1 |paste -  tax_temp.txt > tax_temp2.txt
echo "Feature ID\tTaxon" > tax.txt
sed -i '1d' tax_temp2.txt
cat tax_temp2.txt >> tax.txt
# 格式转换
  biom convert -i meta.txt \
  -o metaphlan.biom  --to-hdf5 --table-type="OTU table"
# 导入特征表
qiime tools import --input-path metaphlan.biom \
  --type 'FeatureTable[Frequency]' --input-format BIOMV210Format \
  --output-path zfg_table.qza
qiime tools import --input-path tax.txt \
  --type 'FeatureData[Taxonomy]' --input-format TSVTaxonomyFormat \
  --output-path zfg_tax.qza
# 堆叠柱状图展示
qiime taxa barplot \
  --i-table zfg_table.qza \
  --i-taxonomy zfg_tax.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization taxa-bar-plots.qzv
# 属
  qiime taxa collapse \
  --i-table zfg_table.qza \
  --i-taxonomy zfg_tax.qza \
  --p-level 6 \
  --o-collapsed-table table-l6.qza
# 多样性
for a in ace shannon simpson
do
qiime diversity alpha \
 --i-table table-l6.qza \
 --p-metric $a \
 --o-alpha-diversity ${a}.qza 
 qiime diversity alpha-group-significance \
  --i-alpha-diversity ${a}.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization alpha/${a}_group.qzv
 done
 
 for b in braycurtis jaccard 
do
qiime diversity beta \
 --i-table table-l6.qza \
 --p-metric $b \
 --o-distance-matrix ${b}.qza 
# qiime diversity adonis \
#  --i-distance-matrix ${b}.qza \
#  --m-metadata-file sample-metadata.tsv \
#  --p-formula 
#  --o-visualization ${b}_adonis.qza
qiime diversity beta-group-significance \
 --i-distance-matrix ${b}.qza \
 --m-metadata-file sample-metadata.tsv \
 --m-metadata-column Group \
 --o-visualization alpha/${b}_group.qzv
 
 qiime diversity pcoa \
   --i-distance-matrix ${b}.qza \
   --o-pcoa ${b}_pcoa.qza
 
 qiime emperor plot \
  --i-pcoa ${b}_pcoa.qza \
  --m-metadata-file sample-metadata.tsv \
  --o-visualization ${b}.qzv
 
 done