Combine MicrobIEM decontamination output (as a .tsv file) with Qiime2 rep-seqs, feature-table, and taxonomy output (as .tsv files)
To use this script you will need to have done the following:
Files needed:
feature-table.qza
taxonomy.qza
rep-seqs.qza
#makes a biom_file directory and makes a feature-table.biom file
qiime tools export --input-path feature-table.qza --output-path biom_file
#converts the .biom file to a tsv file of the feature table
biom convert -i feature-table.biom -o feature-table.tsv --table-type="OTU table" --to-tsv
#makes a taxonomy directory with a taxonomy tsv file
qiime tools export --input-path taxonomy.qza --output-path taxonomy
#To convert rep-sees to a tsv file, make a sequences.fasta file
qiime tools export
--input-path rep-seqs.qza
--output-path rep-seqs
#makes a rep-seqs tsv file
awk '/^>/ {if (seq) print id"\t"seq; id=substr($0,2); seq=""} /^[^>]/ {seq=seq $0} END {print id"\t"seq}'
dna-sequences.fasta > rep-seqs.tsv
#fix/check headers in resulting tsv files
#rename Feature ID to OTU_ID
vi feature-table.tsv
#rename taxon taxonomy
vi taxonomy.tsv
#add headers
vi rep-seqs.tsv