#!/bin/bash

name=$1
testfa=../testfa/$name
trainfa=../trainfa/$name

if [ ! -f $testfa ] ; then
	echo Not found testfa=$testfa >> /dev/stderr
	exit 1
fi

if [ ! -f $trainfa ] ; then
	echo Not found trainfa=$trainfa >> /dev/stderr
	exit 1
fi

traindir=../train/met/$name
mkdir -p $traindir

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

preddir=../pred/met
mkdir -p $preddir

pred=$preddir/$name

if [ -s $pred ] ; then
	ls -lh $pred
	echo Skipping existing pred=$pred
	exit 0
fi

python2 /zip_e/r/py/fasta_utax2_to_metaxa2.py $trainfa $traindir/db.fa $traindir/tax.txt

metaxa2_dbb -b $traindir/db.fa -o $traindir/outdb -t $traindir/tax.txt --auto_rep T \
  --cpu 6 --mode divergent # > stdout_train.txt 2> stderr_train.txt

metaxa2 -i $testfa -d $traindir/outdb/blast -p $traindir/outdb/HMMs \
  -o $traindir/results -cpu 6 # > stdout_test.txt 2> stderr_test.txt

cat $traindir/results.taxonomy.txt > $raw

python2 /zip_e/r/py/metaxa2tab.py $raw $testfa > $pred