74 lines
2.6 KiB
Plaintext
74 lines
2.6 KiB
Plaintext
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#!/usr/bin/env python
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"""
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Copyright 2015, Daehwan Kim <infphilo@gmail.com>
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This file is part of HISAT 2.
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HISAT 2 is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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HISAT 2 is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
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"""
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import os
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import imp
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import inspect
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import logging
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def main():
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logging.basicConfig(level=logging.ERROR,
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format='%(levelname)s: %(message)s'
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)
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inspect_bin_name = "hisat2-inspect"
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inspect_bin_s = "hisat2-inspect-s"
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inspect_bin_l = "hisat2-inspect-l"
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idx_ext_l = '.1.ht2l';
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idx_ext_s = '.1.ht2';
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curr_script = os.path.realpath(inspect.getsourcefile(main))
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ex_path = os.path.dirname(curr_script)
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inspect_bin_spec = os.path.join(ex_path,inspect_bin_s)
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bld = imp.load_source('hisat2-build',os.path.join(ex_path,'hisat2-build'))
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options,arguments = bld.build_args()
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if '--verbose' in options:
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logging.getLogger().setLevel(logging.INFO)
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if '--debug' in options:
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inspect_bin_spec += '-debug'
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inspect_bin_l += '-debug'
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if '--large-index' in options:
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inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
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elif len(arguments) >= 1:
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idx_basename = arguments[-1]
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large_idx_exists = os.path.exists(idx_basename + idx_ext_l)
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small_idx_exists = os.path.exists(idx_basename + idx_ext_s)
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if not large_idx_exists and not small_idx_exists:
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env_path = os.getenv('HISAT2_INDEXES', '')
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large_idx_exists = os.path.exists(env_path + '/' + idx_basename + idx_ext_l)
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small_idx_exists = os.path.exists(env_path + '/' + idx_basename + idx_ext_s)
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if large_idx_exists and not small_idx_exists:
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inspect_bin_spec = os.path.join(ex_path,inspect_bin_l)
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arguments[0] = inspect_bin_name
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arguments.insert(1, 'basic-0')
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arguments.insert(1, '--wrapper')
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logging.info('Command: %s %s' % (inspect_bin_spec,' '.join(arguments[1:])))
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os.execv(inspect_bin_spec, arguments)
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if __name__ == "__main__":
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main()
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