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

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

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

pred=$preddir/$name

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

sed "-es/;.*//" < $trainfa > $traindir/db.fa
makeblastdb -in $traindir/db.fa -dbtype nucl -parse_seqids -out $traindir/db

blastn -task megablast -db $traindir/db -query $testfa -num_threads 10 \
  -max_target_seqs 1 -outfmt "6 qseqid sseqid" -evalue 0.01 > $raw