149 lines
4.6 KiB
Python
149 lines
4.6 KiB
Python
#!/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 sys
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import inspect
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import logging
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import re
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def build_args():
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"""
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Parse the wrapper arguments. Returns the options,<programm arguments> tuple.
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"""
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parsed_args = {}
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to_remove = []
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argv = sys.argv[:]
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for i, arg in enumerate(argv):
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if arg == '--large-index':
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parsed_args[arg] = ""
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to_remove.append(i)
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elif arg == '--debug':
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parsed_args[arg] = ""
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to_remove.append(i)
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elif arg == '--verbose':
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parsed_args[arg] = ""
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to_remove.append(i)
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for i in reversed(to_remove):
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del argv[i]
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return parsed_args, argv
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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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delta = 200
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small_index_max_size= 4 * 1024**3 - delta
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build_bin_name = "hisat2-build"
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build_bin_s = "hisat2-build-s"
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build_bin_l = "hisat2-build-l"
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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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build_bin_spec = os.path.join(ex_path,build_bin_s)
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#repeat_bin_spec = os.path.join(ex_path,"hisat2-repeat")
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options, argv = 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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build_bin_spec += '-debug'
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build_bin_l += '-debug'
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if '--large-index' in options:
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build_bin_spec = os.path.join(ex_path,build_bin_l)
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elif len(argv) >= 2:
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ref_fnames = argv[-2]
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tot_size = 0
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for fn in ref_fnames.split(','):
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if os.path.exists(fn):
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statinfo = os.stat(fn)
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tot_size += statinfo.st_size
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if tot_size > small_index_max_size:
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build_bin_spec = os.path.join(ex_path, build_bin_l)
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if "--repeat-index" in argv:
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#build repeat index first
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if argv[1].startswith('-'):
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outputName = argv[-1]
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else:
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outputName = argv[2]
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nThread = "1"
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repeatLength = "100-300"
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repeatCount = "5"
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referenceName = ""
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base_change = ""
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removeRepeatLength = False
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for i in range(len(argv)):
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if argv[i] == "--base-change":
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base_change = argv[i+1]
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if argv[i] == "-p":
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nThread = argv[i+1]
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elif argv[i] == "-f":
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referenceName = argv[i+1]
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elif argv[i] == "--repeat-index":
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if ("--repeat-index" != argv[-1]):
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match = re.match(r'\d+-\d+', argv[i+1])
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if match:
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repeatLength = argv[i+1]
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removeRepeatLength = True
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if removeRepeatLength:
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argv.remove(repeatLength)
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if len(referenceName) == 0:
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if argv[1].startswith('-'):
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referenceName = argv[-2]
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else:
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referenceName = argv[1]
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cwd = sys.path[0]
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repeatArgv = []
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repeatArgv += [cwd + "/hisat2-repeat"]
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repeatArgv += ["-p", nThread]
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repeatArgv += ["--repeat-length", repeatLength]
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repeatArgv += ["--repeat-count", repeatCount]
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repeatArgv += ["--base-change", base_change]
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repeatArgv += ["--3N"]
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repeatArgv += [referenceName, outputName]
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try:
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os.system(" ".join(repeatArgv))
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except ValueError:
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print("Can not automatically generate repeat database for HISAT-3N. Please manually generate repeat database by using hisat2-repeat.")
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argv.append("--3N")
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argv[0] = build_bin_name
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argv.insert(1, 'basic-0')
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argv.insert(1, '--wrapper')
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logging.info('Command: %s %s' % (build_bin_spec, ' '.join(argv[1:])))
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os.execv(build_bin_spec, argv)
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if __name__ == "__main__":
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main()
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