Mercurial > repos > drosofff > parse_srbowtie_alignment

comparison smRtools.py @ 4:945878e8e287 draft

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author drosofff
date Mon, 23 Jun 2014 05:15:24 -0400
parents 27b40e4ccee2
children
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3:27b40e4ccee2 4:945878e8e287
302 '''return a dictionary of number of reads by size (the keys)''' 302 '''return a dictionary of number of reads by size (the keys)'''
303 dicsize = {} 303 dicsize = {}
304 for offset in self.readDict: 304 for offset in self.readDict:
305 for size in self.readDict[offset]: 305 for size in self.readDict[offset]:
306 dicsize[size] = dicsize.get(size, 0) + 1 306 dicsize[size] = dicsize.get(size, 0) + 1
307 for offset in range (min(dicsize.keys(), max(dicsize.keys()+1): 307 for offset in range (min(dicsize.keys()), max(dicsize.keys())+1):
308 dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values 308 dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
309 return dicsize 309 return dicsize
310 310
311 def statsizes (self, upstream_coord=None, downstream_coord=None): 311 def statsizes (self, upstream_coord=None, downstream_coord=None):
312 ''' migration to memory saving by specifying possible subcoordinates 312 ''' migration to memory saving by specifying possible subcoordinates