Package Bio :: Package SeqIO :: Module AbiIO
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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...
  _INSTRUMENT_SPECIFIC_TAGS = {'abi_3130/3130xl': {'CTOw1': 'Con...
  _BYTEFMT = {1: 'b', 2: 's', 3: 'H', 4: 'h', 5: 'i', 6: '2i', 7...
  _HEADFMT = '>H4sI2H3I'
  _DIRFMT = '>4sI2H4I'
  __global_tag_listing = ['BufT1', 'ScPa1', 'ASPt1', 'ASPt2', 'P...
  __package__ = 'Bio.SeqIO'
  tag = {'APFN2': 'Sequencing Analysis parameters file name', 'A...
Function Details [hide private]

_abi_trim(seq_record)

source code 

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

Arguments:
  • 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.

Arguments:
  • 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'}

_INSTRUMENT_SPECIFIC_TAGS

Value:
{'abi_3130/3130xl': {'CTOw1': 'Container owner',
                     'HCFG1': 'Instrument Class',
                     'HCFG2': 'Instrument Family',
                     'HCFG3': 'Official Instrument Name',
                     'HCFG4': 'Instrument Parameters',
                     'RMdVa1': 'Run Module version'},
 'abi_3530/3530xl': {'AAct1': 'Primary Analysis Audit Active indicatio\
n. True if system auditing was enabled during the last write of this f\
...

_BYTEFMT

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

__global_tag_listing

Value:
['BufT1',
 'ScPa1',
 'ASPt1',
 'ASPt2',
 'PCON1',
 'PCON2',
 'ABLt1',
 'AmbT1',
...

tag

Value:
{'APFN2': 'Sequencing Analysis parameters file name',
 'APXV1': 'Analysis Protocol XML schema version',
 'APrN1': 'Analysis Protocol settings name',
 'APrV1': 'Analysis Protocol settings version',
 'APrX1': 'Analysis Protocol XML string',
 'CMNT1': 'Sample Comment',
 'CTID1': 'Container Identifier, a.k.a. plate barcode',
 'CTNM1': 'Container name, usually identical to CTID, but not necessar\
...