CloneSet48

Bio/SeqIO/_convert.py

Bio/SeqIO/_convert.py

Bio/SeqIO/_convert.py

Bio/SeqIO/_convert.py

    """Fast Sanger FASTQ to Sanger FASTQ conversion (PRIVATE).

    Useful for removing line wrapping and the redundant second identifier
    on the plus lines. Will check also check the quality string is valid.

    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 
    #Map unexpected chars to null
    mapping = "".join([chr(0) for ascii in range(0,33)]+[chr(ascii) for ascii in range(33,127)]+[chr(0) for ascii in range(127,256)]) 


    assert len(mapping)==256 
    return _fastq_generic(in_handle,out_handle,mapping) 

    """Fast Solexa FASTQ to Solexa FASTQ conversion (PRIVATE).

    Useful for removing line wrapping and the redundant second identifier
    on the plus lines. Will check also check the quality string is valid.
    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 
    #Map unexpected chars to null
    mapping = "".join([chr(0) for ascii in range(0,59)]+[chr(ascii) for ascii in range(59,127)]+[chr(0) for ascii in range(127,256)]) 


    assert len(mapping)==256 
    return _fastq_generic(in_handle,out_handle,mapping) 

    """Fast Illumina 1.3+ FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE).

    Useful for removing line wrapping and the redundant second identifier
    on the plus lines. Will check also check the quality string is valid.
    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 
    #Map unexpected chars to null
    mapping = "".join([chr(0) for ascii in range(0,64)]+[chr(ascii) for ascii in range(64,127)]+[chr(0) for ascii in range(127,256)]) 


    assert len(mapping)==256 
    return _fastq_generic(in_handle,out_handle,mapping) 

    """Fast Illumina 1.3+ FASTQ to Sanger FASTQ conversion (PRIVATE).

    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 
    #Map unexpected chars to null
    mapping = "".join([chr(0) for ascii in range(0,64)]+[chr(33+q) for q in range(0,62+1)]+[chr(0) for ascii in range(127,256)]) 


    assert len(mapping)==256 
    return _fastq_generic(in_handle,out_handle,mapping) 

   [[#variable5d75bf00]]
  #Map unexpected chars to null
  mapping = "".join([chr(0) for ascii in range(0, [[#variable5cdd6be0]])]+[chr( [[#variable30589400]]) for [[#variable2f2aae60]]in range( [[#variable71ac3280]], [[#variable5d75bf40]])]+[chr(0) for ascii in range(127,256)]) 
  assert len(mapping)==256 
  return _fastq_generic(in_handle,out_handle,mapping) 
 

"""Fast Sanger FASTQ to Sanger FASTQ conversion (PRIVATE).

    Useful for removing line wrapping and the redundant second identifier
    on the plus lines. Will check also check the quality string is valid.

    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 

"""Fast Solexa FASTQ to Solexa FASTQ conversion (PRIVATE).

    Useful for removing line wrapping and the redundant second identifier
    on the plus lines. Will check also check the quality string is valid.
    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 

"""Fast Illumina 1.3+ FASTQ to Illumina 1.3+ FASTQ conversion (PRIVATE).

    Useful for removing line wrapping and the redundant second identifier
    on the plus lines. Will check also check the quality string is valid.
    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 

"""Fast Illumina 1.3+ FASTQ to Sanger FASTQ conversion (PRIVATE).

    Avoids creating SeqRecord and Seq objects in order to speed up this
    conversion.
    """ 

33 

59 

64 

64 

ascii 

ascii 

ascii 

33+q 

ascii 

ascii 

ascii 

q 

33 

59 

64 

0 

127 

127 

127 

62+1