comparison snpEff_cds_report.py @ 1:29b286896c50

Change the default number of Amino Acids to display after a missense to 10.

0:cdbdac66d6b5

        end_pos = len(var_aa)
      novel_peptide = var_aa[var_aa_pos:end_pos]
      return novel_peptide
    return None
  # [preAA,varAA,postAA, varPeptide, varOffset, subAA]
  def getNonSynonymousPeptide(self,start_offset,end_offset,toStopCodon=True):
    (coding_seq, alt_seq, pos, coding_aa, var_aa, var_aa_pos, var_aa_end) = self.getSequences()
    if var_aa:
      start_pos = max(var_aa_pos - start_offset,0) if start_offset and int(start_offset) >= 0 else 0
      if toStopCodon:
        end_pos = var_aa_end
      else:
        end_pos = min(var_aa_pos+end_offset,len(var_aa)) if end_offset and int(end_offset) >= 0 else var_aa_end
      try:
        varAA = var_aa[var_aa_pos] if var_aa_pos < len(var_aa) else '_' 
        if debug: print >> sys.stdout, "HGVS %s %s pos:\t%d %d %d" % (self.transcript, self.effect, start_pos, var_aa_pos, end_pos)
        mutation = "p.%s%d%s" % (coding_aa[var_aa_pos],var_aa_pos+1,varAA)

1:29b286896c50

        end_pos = len(var_aa)
      novel_peptide = var_aa[var_aa_pos:end_pos]
      return novel_peptide
    return None
  # [preAA,varAA,postAA, varPeptide, varOffset, subAA]
  def getNonSynonymousPeptide(self,start_count,end_count,toStopCodon=True):
    (coding_seq, alt_seq, pos, coding_aa, var_aa, var_aa_pos, var_aa_end) = self.getSequences()
    if var_aa:
      start_pos = max(var_aa_pos - start_count,0) if start_count and int(start_count) >= 0 else 0
      if toStopCodon:
        end_pos = var_aa_end
      else:
        end_offset = end_count + 1
        end_pos = min(var_aa_pos+end_offset,len(var_aa)) if end_offset and int(end_offset) >= 0 else var_aa_end
      try:
        varAA = var_aa[var_aa_pos] if var_aa_pos < len(var_aa) else '_' 
        if debug: print >> sys.stdout, "HGVS %s %s pos:\t%d %d %d" % (self.transcript, self.effect, start_pos, var_aa_pos, end_pos)
        mutation = "p.%s%d%s" % (coding_aa[var_aa_pos],var_aa_pos+1,varAA)