#!/bin/bash

name=$1

qfa=../testfa/$name
dbfa=../trainfa/$name

mkdir -p ../date
mydate > ../date/q2b.$name

rawdir=../raw/q2b
mkdir -p $rawdir
raw=$rawdir/$name

preddir=../pred/q2b
mkdir -p $preddir
pred=../pred/q2b/$name

# Must be at same level as scripts/
tmpdir=../tmp_q2b.$$.$RANDOM
mkdir -p $tmpdir
cd $tmpdir

python2 $r/py/fasta_utax2qiime.py $dbfa dbq.fa db-tax.txt

export LC_ALL=C.UTF-8
export LANG=C.UTF-8
source activate qiime2-2017.10

qiime tools import \
  --input-path $qfa \
  --output-path q-seqs.qza \
  --type 'FeatureData[Sequence]'

qiime tools import \
  --input-path dbq.fa \
  --output-path db-seqs.qza \
  --type 'FeatureData[Sequence]'

qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --source-format HeaderlessTSVTaxonomyFormat \
  --input-path db-tax.txt \
  --output-path db-tax.qza

qiime feature-classifier classify-consensus-blast \
  --i-query q-seqs.qza \
  --i-reference-reads db-seqs.qza \
  --i-reference-taxonomy db-tax.qza \
  --o-classification classifier_output.qza

qiime tools export \
	classifier_output.qza \
	--output-dir output_dir

cp -v output_dir/taxonomy.tsv $raw

python2 $r/py/qiime2tax2tab.py $raw > $pred

mydate >> ../date/q2b.$name

rm -rf $tmpdir