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NCBIClassifier.sh
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NCBIClassifier.sh
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#!/bin/sh
## the NCBI files
cat 16S_id_to_taxModDone.map | awk -F '[;\t]' '{print $1 "\t" "k__" $2 ";p__" $3 ";c__" $4 ";o__" $5 ";f__" $6 ";g__" $7 ";s__" $8 ";ss__" $9 }' > working2019.map
cat 16SMicrobial.fasta > working2019.fasta
## code correct for the QIIME2 2019.1 version
qiime tools import --input-path working2019.fasta --output-path workingSeqs2019.qza --type 'FeatureData[Sequence]'
qiime tools import --type 'FeatureData[Taxonomy]' --input-format HeaderlessTSVTaxonomyFormat --input-path working2019.map --output-path workingTaxonomy2019.qza
qiime feature-classifier extract-reads --i-sequences workingSeqs2019.qza --p-f-primer CCTACGGGAGGCAGCAG --p-r-primer GGACTACHVGGGTWTCTAAT --o-reads workingSeqsExtracted2019.qza
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads workingSeqsExtracted2019.qza --i-reference-taxonomy workingTaxonomy2019.qza --o-classifier workingClassifier.qza