comparison smRtools.py @ 8:be0c6b6466cc draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 97b40d7a593cef6c3303f7baba781a84d242e454

7:c9e267cb84c0

        else:
          self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
          self.alignedReads += 1
      F.close()
      return self.instanceDict
#    elif self.alignmentFileFormat == "sam":
#      F = open (self.alignmentFile, "r")
#      dict = {"0":"+", "16":"-"}
#      for line in F:
#        if line[0]=='@':
#            continue
#        fields = line.split()
#        if fields[2] == "*": continue
#        polarity = dict[fields[1]]
#        gene = fields[2]
#        offset = int(fields[3])
#        size = len (fields[9])
#        if self.size_inf:
#          if (size>=self.size_inf and size<= self.size_sup):
#            self.instanceDict[gene].addread (polarity, offset, size)
#            self.alignedReads += 1
#       else:
#          self.instanceDict[gene].addread (polarity, offset, size)
#          self.alignedReads += 1
#      F.close()
    elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam":
      import pysam
      samfile = pysam.Samfile(self.alignmentFile)
      for read in samfile:
        if read.tid == -1:

        else:
          self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
          self.alignedReads += 1
      return self.instanceDict

#  def size_histogram (self):
#    size_dict={}
#    size_dict['F']= defaultdict (int)
#    size_dict['R']= defaultdict (int)
#    size_dict['both'] = defaultdict (int)
#    for item in self.instanceDict:
#      buffer_dict_F = self.instanceDict[item].size_histogram()['F']
#      buffer_dict_R = self.instanceDict[item].size_histogram()['R']
#      for size in buffer_dict_F:
#        size_dict['F'][size] += buffer_dict_F[size]
#      for size in buffer_dict_R:
#        size_dict['R'][size] -= buffer_dict_R[size]
#    allSizeKeys = list (set (size_dict['F'].keys() + size_dict['R'].keys() ) )
#    for size in allSizeKeys:
#      size_dict['both'][size] = size_dict['F'][size] + size_dict['R'][size]
#    return size_dict
  def size_histogram (self): # in HandleSmRNAwindows
    '''refactored on 7-9-2014 to debug size_histogram tool'''
    size_dict={}
    size_dict['F']= defaultdict (float)
    size_dict['R']= defaultdict (float)

      for size in self.readDict[offset]:
        dicsize[size] = dicsize.get(size, 0) + 1
    for offset in range (min(dicsize.keys()), max(dicsize.keys())+1):
      dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
    return dicsize
    
#  def size_histogram(self):
#    norm=self.norm
#    hist_dict={}
#    hist_dict['F']={}
#    hist_dict['R']={}
#    for offset in self.readDict:
#      for size in self.readDict[offset]:
#        if offset < 0:
#          hist_dict['R'][size] = hist_dict['R'].get(size, 0) - 1*norm
#        else:
#          hist_dict['F'][size] = hist_dict['F'].get(size, 0) + 1*norm
#   ## patch to avoid missing graphs when parsed by R-lattice. 27-08-2014. Test and validate !    
#    if not (hist_dict['F']) and (not hist_dict['R']):
#      hist_dict['F'][21] = 0
#      hist_dict['R'][21] = 0
#   ##
#    return hist_dict

  def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow
    '''refactored on 7-9-2014 to debug size_histogram tool'''
    norm=self.norm
    size_dict={}

      return "%s | ." % (freqDic["Tfor"] / forward_sum * 100)
    elif forward_sum == 0:
      return ". | %s" % (freqDic["Trev"] / reverse_sum * 100)
    else:
      return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100)

    
  def readplot (self):
    norm=self.norm
    readmap = {}
    for offset in self.readDict.keys():

8:be0c6b6466cc

        else:
          self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
          self.alignedReads += 1
      F.close()
      return self.instanceDict
    elif self.alignmentFileFormat == "bam" or self.alignmentFileFormat == "sam":
      import pysam
      samfile = pysam.Samfile(self.alignmentFile)
      for read in samfile:
        if read.tid == -1:

        else:
          self.instanceDict[gene].addread (polarity, offset+1, size) # to correct to 1-based coordinates of SmRNAwindow
          self.alignedReads += 1
      return self.instanceDict

  def size_histogram (self): # in HandleSmRNAwindows
    '''refactored on 7-9-2014 to debug size_histogram tool'''
    size_dict={}
    size_dict['F']= defaultdict (float)
    size_dict['R']= defaultdict (float)

      for size in self.readDict[offset]:
        dicsize[size] = dicsize.get(size, 0) + 1
    for offset in range (min(dicsize.keys()), max(dicsize.keys())+1):
      dicsize[size] = dicsize.get(size, 0) # to fill offsets with null values
    return dicsize


  def size_histogram(self, minquery=None, maxquery=None): # in SmRNAwindow
    '''refactored on 7-9-2014 to debug size_histogram tool'''
    norm=self.norm
    size_dict={}

      return "%s | ." % (freqDic["Tfor"] / forward_sum * 100)
    elif forward_sum == 0:
      return ". | %s" % (freqDic["Trev"] / reverse_sum * 100)
    else:
      return "%s | %s" % (freqDic["Tfor"] / forward_sum * 100, freqDic["Trev"] / reverse_sum * 100)
    
  def readplot (self):
    norm=self.norm
    readmap = {}
    for offset in self.readDict.keys():