Mercurial > repos > drosofff > mi_rna_parser

comparison smRtools.py @ 5:59dfb33ca70e draft

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author drosofff
date Mon, 23 Jun 2014 05:14:35 -0400
parents 9f17e8fc1d28
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4:ac8fd41b8c98 5:59dfb33ca70e
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):
308 dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
307 return dicsize 309 return dicsize
308 310
309 def statsizes (self, upstream_coord=None, downstream_coord=None): 311 def statsizes (self, upstream_coord=None, downstream_coord=None):
310 ''' migration to memory saving by specifying possible subcoordinates 312 ''' migration to memory saving by specifying possible subcoordinates
311 see the readcount method for further discussion''' 313 see the readcount method for further discussion'''
391 if readmap[offset][0] != 0: 393 if readmap[offset][0] != 0:
392 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, -readmap[offset][0], "R") ) 394 mylist.append("%s\t%s\t%s\t%s" % (self.gene, offset, -readmap[offset][0], "R") )
393 return mylist 395 return mylist
394 396
395 def readcoverage (self, upstream_coord=None, downstream_coord=None, windowName=None): 397 def readcoverage (self, upstream_coord=None, downstream_coord=None, windowName=None):
396 '''This method has not been tested yet 15-11-2013''' 398 '''Use by MirParser tool'''
397 upstream_coord = upstream_coord or 1 399 upstream_coord = upstream_coord or 1
398 downstream_coord = downstream_coord or self.size 400 downstream_coord = downstream_coord or self.size
399 windowName = windowName or "%s_%s_%s" % (self.gene, upstream_coord, downstream_coord) 401 windowName = windowName or "%s_%s_%s" % (self.gene, upstream_coord, downstream_coord)
400 forORrev_coverage = dict ([(i,0) for i in xrange(1, downstream_coord-upstream_coord+1)]) 402 forORrev_coverage = dict ([(i,0) for i in xrange(1, downstream_coord-upstream_coord+1)])
401 totalforward = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="forward") 403 totalforward = self.readcount(upstream_coord=upstream_coord, downstream_coord=downstream_coord, polarity="forward")