#!/usr/bin/env python
# Copyright (C) The Arvados Authors. All rights reserved.
#
# SPDX-License-Identifier: Apache-2.0

import arvados
import os
import re
import sys
import pyrtg

this_job = arvados.current_job()
this_task = arvados.current_task()
fasta_path = arvados.util.collection_extract(
    collection = this_job['script_parameters']['input'],
    path = 'fasta',
    decompress = False)
fasta_files = filter(lambda f: f != '.locator', os.listdir(fasta_path))
out_dir = os.path.join(arvados.current_task().tmpdir, 'ref-sdf')
arvados.util.run_command(['rm', '-rf', out_dir], stderr=sys.stderr)

pyrtg.run_rtg('format', out_dir,
              map(lambda f: os.path.join(fasta_path, f), fasta_files))

out = arvados.CollectionWriter()
out.write_directory_tree(out_dir, max_manifest_depth=0)
this_task.set_output(out.finish())