#!/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/blca/$name
mkdir -p $traindir

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

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

pred=$preddir/$name

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

export PATH=/p/sw/blast2.5.0:$PATH

if [ ! -s $traindir/db.nsq ] ; then
	python2 /zip_e/r/py/fasta_utax2_to_blca.py $trainfa $traindir/db.fa $traindir/tax.txt
	makeblastdb -in $traindir/db.fa -dbtype nucl -parse_seqids -out $traindir/db
fi

python2 /zip_e/r/py/fasta_utax2_to_blca.py $testfa $traindir/q.fa $traindir/qtax.txt

python2 /p/sw/blca/2.blca_main.py -i $traindir/q.fa -r $traindir/tax.txt -q $traindir/db

cat $traindir/q.fa.blca.out > $raw

python2 /zip_e/r/py/blca2tab.py $raw $testfa > $pred