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#!/usr/bin/env python
################################################################################
#
#
# combinatorics.py
#
# Copyright (c) 2013 Leo Goodstadt
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#################################################################################
"""
********************************************
:mod:`ruffus.combinatorics` -- Overview
********************************************
.. moduleauthor:: Leo Goodstadt <ruffus@llew.org.uk>
#
# @product
#
from ruffus import *
@product(
"/a_directory/dataset1.*.bam",
formatter( ".*/dataset1\.(?P<ID>\d+).bam" ),
"/a_different/directory/dataset2.*.bam",
formatter(".species", ".*/dataset2\.(?P<ID>\d+).bam" ),
"{path[0][0]}/{base_name[0][0]}.{base_name[0][0]}.out",
"{path[0][0]}", # extra: path for 1st input, 1st file
"{path[1][0]}", # extra: path for 2nd input, 1st file
"{basename[0][1]}", # extra: file name for 1st input, 2nd file
"{ID[1][1]}", # extra: regular expression named capture group for 2nd input, 2nd file
)
def task1( infiles, outfile,
input_1__path,
input_2__path,
input_1__2nd_file_name,
input_2__3rd_file_match
):
print infiles
print outfile
print input_1__path
print input_2__path
print input_1__2nd_file_name
print input_2__3rd_file_match
"""
from .task import task_decorator
#
# Combinatoric generators:
#
class product(task_decorator):
pass
class permutations(task_decorator):
pass
class combinations(task_decorator):
pass
class combinations_with_replacement(task_decorator):
pass
|
