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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 target_breakdown(filename, maxRegionSize, targetRegionSize, out_fname):
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25 from math import ceil
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26
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27 a = open(filename)
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28 output = open(out_fname, "w")
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29
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30 for x in a:
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31 x = x.split()
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32 chr = x[0]
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33 start = int(x[1])
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34 end = int(x[2])
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35 info = ""
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36 if (len(x) > 3):
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37 info = x[3]
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38
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39 regionSize = end-start
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40
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41 if regionSize > maxRegionSize:
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42 seg = ceil(regionSize/float(targetRegionSize))
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43 limit = ceil(regionSize/float(seg))
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44
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45 s_end = start
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46 for i in range(int(seg)):
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47 s_start = s_end
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48 s_end = int(start + (limit*(i+1)))
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49 if s_end > end:
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50 s_end = end
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51 output.write("\t".join([chr, str(s_start), str(s_end), info+"(SPLIT)"])+"\n")
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52 else:
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53 output.write("\t".join([chr, str(start), str(end), info])+"\n")
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54
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55 output.close()
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56
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