Package Bio :: Package SeqIO :: Module AbiIO
[hide private]
[frames] | no frames]

Module AbiIO

source code

Bio.SeqIO parser for the ABI format.

ABI is the format used by Applied Biosystem's sequencing machines to store sequencing results.

For more details on the format specification, visit: http://www.appliedbiosystem.com/support/software_community/ABIF_File_Format.pdf

Functions [hide private]
 
AbiIterator(handle, alphabet=None, trim=False)
Iterator for the Abi file format.
source code
 
_AbiTrimIterator(handle)
Iterator for the Abi file format that yields trimmed SeqRecord objects.
source code
 
_abi_parse_header(header, handle)
Generator that returns directory contents.
source code
 
_abi_trim(seq_record)
Trims the sequence using Richard Mott's modified trimming algorithm.
source code
 
_parse_tag_data(elem_code, elem_num, raw_data)
Returns single data value.
source code
Variables [hide private]
  _EXTRACT = {'DySN1': 'dye', 'GTyp1': 'polymer', 'MODL1': 'mach...
  _SPCTAGS = ['PBAS2', 'PCON2', 'SMPL1', 'RUND1', 'RUND2', 'RUNT...
  _BYTEFMT = {1: 'b', 2: 's', 3: 'H', 4: 'h', 5: 'i', 6: '2i', 7...
  _HEADFMT = '>H4sI2H3I'
  _DIRFMT = '>4sI2H4I'
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

_abi_trim(seq_record)

source code 

Trims the sequence using Richard Mott's modified trimming algorithm.

seq_record - SeqRecord object to be trimmed.

Trimmed bases are determined from their segment score, which is a cumulative sum of each base's score. Base scores are calculated from their quality values.

More about the trimming algorithm: http://www.phrap.org/phredphrap/phred.html http://www.clcbio.com/manual/genomics/Quality_abif_trimming.html

_parse_tag_data(elem_code, elem_num, raw_data)

source code 

Returns single data value.

elem_code - What kind of data elem_num - How many data points raw_data - abi file object from which the tags would be unpacked


Variables Details [hide private]

_EXTRACT

Value:
{'DySN1': 'dye',
 'GTyp1': 'polymer',
 'MODL1': 'machine_model',
 'TUBE1': 'sample_well'}

_SPCTAGS

Value:
['PBAS2', 'PCON2', 'SMPL1', 'RUND1', 'RUND2', 'RUNT1', 'RUNT2']

_BYTEFMT

Value:
{1: 'b',
 2: 's',
 3: 'H',
 4: 'h',
 5: 'i',
 6: '2i',
 7: 'f',
 8: 'd',
...