def _fastq_convert_qual(in_handle, out_handle, mapping):
 from Bio.SeqIO.QualityIO import FastqGeneralIterator
 count = 0
 for (title, seq, qual) in FastqGeneralIterator(in_handle):
  count += 1
  out_handle.write(('>%s\n' % title))
  try:
   qualities_strs = [mapping[ascii] for ascii in qual]
  except KeyError:
   raise ValueError('Invalid character in quality string')
  data = ' '.join(qualities_strs)
  while (len(data) > 60):
   if (data[60] == ' '):
    out_handle.write((data[:60] + '\n'))
    data = data[61:]
   elif (data[59] == ' '):
    out_handle.write((data[:59] + '\n'))
    data = data[60:]
   else:
    assert (data[58] == ' '), 'Internal logic failure in wrapping'
    out_handle.write((data[:58] + '\n'))
    data = data[59:]
  out_handle.write((data + '\n'))
 return count

def _fastq_convert_qual ( in_handle , out_handle , mapping ) : from Bio . SeqIO . QualityIO import FastqGeneralIterator count = 0 for ( title , seq , qual ) in FastqGeneralIterator ( in_handle ) : count += 1 out_handle . write ( ( '>%s\n' % title ) ) try : qualities_strs = [ mapping [ ascii ] for ascii in qual ] except KeyError : raise ValueError ( 'Invalid character in quality string' ) data = ' ' . join ( qualities_strs ) while ( len ( data ) > 60 ) : if ( data [ 60 ] == ' ' ) : out_handle . write ( ( data [ : 60 ] + '\n' ) ) data = data [ 61 : ] elif ( data [ 59 ] == ' ' ) : out_handle . write ( ( data [ : 59 ] + '\n' ) ) data = data [ 60 : ] else : assert ( data [ 58 ] == ' ' ) , 'Internal logic failure in wrapping' out_handle . write ( ( data [ : 58 ] + '\n' ) ) data = data [ 59 : ] out_handle . write ( ( data + '\n' ) ) return count
fastq helper function for qual output .