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1 # ----------------------------------------------------------------------#
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2 # Copyright (c) 2011, Richard Lupat & Jason Li.
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3 #
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4 # > Source License <
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5 # This file is part of CONTRA.
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6 #
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7 # CONTRA is free software: you can redistribute it and/or modify
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8 # it under the terms of the GNU General Public License as published by
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9 # the Free Software Foundation, either version 3 of the License, or
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10 # (at your option) any later version.
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11 #
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12 # CONTRA is distributed in the hope that it will be useful,
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13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 # GNU General Public License for more details.
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16 #
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17 # You should have received a copy of the GNU General Public License
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18 # along with CONTRA. If not, see <http://www.gnu.org/licenses/>.
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19 #
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20 #
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21 #-----------------------------------------------------------------------#
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22 # Last Updated : 05 October 2011 16:43PM
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23
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24 def get_libsize(bedgraph_file):
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25 bedgraph = open(bedgraph_file)
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26 libsize = 0
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27 for line in bedgraph:
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28 line = line.split()
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29 chr = line[0]
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30 start = int(line[1])
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31 end = int(line[2])
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32 cov = float(line[3])
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33 #cov = int(line[3])
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34
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35 libsize += (end-start)*cov
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36
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37 bedgraph.close()
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38 return int(libsize)
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