/usr/lib/python2.7/dist-packages/cogent/app/sfffile.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 | #!/usr/bin/env python
from cogent.app.parameters import FlagParameter, ValuedParameter
from cogent.app.util import CommandLineApplication, ResultPath
"""Application controller for sfffile"""
__author__ = "Kyle Bittinger"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Kyle Bittinger"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Kyle Bittinger"
__email__ = "kylebittinger@gmail.com"
__status__ = "Prototype"
class Sfffile(CommandLineApplication):
"""Simple sfffile application controller.
"""
_options = {
# output filepath
'-o': ValuedParameter('-', 'o', Delimiter=' '),
# file of accession numbers to be included
'-i': ValuedParameter('-', 'i', Delimiter=' '),
# file of accession numbers to be excluded
'-e': ValuedParameter('-', 'e', Delimiter=' '),
# file of custom trim points
'-t': ValuedParameter('-', 't', Delimiter=' '),
# number of cycles in output sff
'-c': ValuedParameter('-', 'c', Delimiter=' '),
# shortcut for -c 42
'-gs20': FlagParameter('-', 'gs20'),
# shortcut for -c 100
'-gsflx': FlagParameter('-', 'gsflx'),
# split multiplexed reads
'-s': ValuedParameter('-', 's', Delimiter=' '),
# custom MID configuration file
'-mcf': ValuedParameter('-', 'mcf', Delimiter=' '),
# prevent propagation of sff index
'-nmft': FlagParameter('-', 'nmft'),
}
_parameters = {}
_parameters.update(_options)
_input_handler = '_input_as_path'
_command = 'sfffile'
def _get_result_paths(self, data):
"""Collect the resultant SFF file in the results.
Because cogent.app.util.CommandLineAppResult opens output
files in text mode, this method may not be portable for
Windows users. A more portable solution would be to not use
the app controller results, but instead specify the output SFF
filepath manually via the '-o' parameter.
"""
if self.Parameters['-o'].isOn():
sff_path = self.Parameters['-o'].Value
else:
sff_path = '454Reads.sff'
return {'sff': ResultPath(sff_path)}
def _accept_exit_status(self, exit_status):
"""Accept an exit status of 0 for the sfffile program.
"""
return exit_status == 0
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