#!/bin/bash

name=$1

preddir=`realpath ../pred/knn`
mkdir -p $preddir
pred=$preddir/$name

rawdir=`realpath ../raw/knn`
mkdir -p $rawdir
raw=$rawdir/$name

mkdir -p ../train/knn/$name
traindir=`realpath ../train/knn/$name`
rm -rf $traindir
mkdir -p $traindir

q=`realpath ../testfa/$name`
db=`realpath ../trainfa/$name`

cd $traindir

cp $q q.fa

mothur_make_taxtrainfiles.py $db dbmot.fa dbtax.txt

$mothur "#classify.seqs(fasta=q.fa, template=dbmot.fa, taxonomy=dbtax.txt, \
  method=knn, processors=6)" > $tmpdir/stdout.txt 2> $tmpdir/stderr.txt

/bin/cp -v q.dbtax.knn.taxonomy $raw

python2 $r/py/motknn2utax2.py $raw > $pred