mkdir training-feature-classifier
cd training-feature-classifier


wget https://files.plutof.ut.ee/doi/0F/6F/0F6F4C85C2553655B6E2B4A0F0BF85AE64A2F769BD82A32053CDEC8708454057.zip
unzip 0F6F4C85C2553655B6E2B4A0F0BF85AE64A2F769BD82A32053CDEC8708454057.zip


awk '/^>/ {print($0)}; /^[^>]/ {print(toupper($0))}' developer/sh_refs_qiime_ver8_99_s_02.02.2019_dev.fasta  > sh_refs_qiime_ver8_99_s_02.02.2019_dev_up.fasta 


sed "s/^[ \t]*//" -i developer/sh_refs_qiime_ver8_99_s_02.02.2019_dev_up.fasta 
 > developer/sh_refs_qiime_ver8_99_s_02.02.2019_dev_uppercase.fasta 


 qiime tools import \
 --type FeatureData[Sequence] \
 --input-path developer/sh_refs_qiime_ver8_99_s_02.02.2019_dev_uppercase.fasta \
 --output-path unite-ver8-99-seqs-02.02.2019.qza


qiime tools import \
 --type FeatureData[Taxonomy] \
 --input-path developer/sh_taxonomy_qiime_ver8_99_s_02.02.2019_dev.txt \
 --output-path unite-ver8-99-taxonomy-s_02.02.2019.qza \
 --input-format HeaderlessTSVTaxonomyFormat


qiime feature-classifier fit-classifier-naive-bayes \
 --i-reference-reads unite-ver8-99-seqs-02.02.2019.qza \
 --i-reference-taxonomy unite-ver8-99-taxonomy-s_02.02.2019.qza \
 --o-classifier unite-ver8-99-classifier-02.02.2019.qza