37 lines
1.1 KiB
Python
37 lines
1.1 KiB
Python
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import farm_commands
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import os.path
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import sys
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from optparse import OptionParser
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from datetime import date
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import glob
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import operator
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if __name__ == "__main__":
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usage = "usage: %prog files"
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parser = OptionParser(usage=usage)
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parser.add_option("-s", "--size", dest="regionSize",
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type="int", default=None, help="")
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(OPTIONS, args) = parser.parse_args()
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def extract(line):
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s = line.split()
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t = s[0].split(":")
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if len(t) == 2:
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chr, pos = t
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return chr, int(pos)
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else:
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return None, None
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for file in args:
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chr, lastPos, startPos, calledBases, progress = None, None, None, None, None
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lastLine = None
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for line in open(file):
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if startPos == None:
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chr, startPos = extract(line)
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lastLine = line
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if lastLine <> None and startPos <> None:
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lastPos = extract(lastLine)[1]
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calledBases = lastPos - startPos
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progress = "%.2f" % (float(calledBases) / OPTIONS.regionSize * 100)
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print file, chr, startPos, lastPos, calledBases, progress
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