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:

Functions [hide private]
AbiIterator(handle, alphabet=None, trim=False)
Return an iterator for the Abi file format.
source code
Return an iterator for the Abi file format that yields trimmed SeqRecord objects (PRIVATE).
source code
_abi_parse_header(header, handle)
Return directory contents (PRIVATE).
source code
Trims the sequence using Richard Mott's modified trimming algorithm (PRIVATE).
source code
_parse_tag_data(elem_code, elem_num, raw_data)
Return single data value (PRIVATE).
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]


source code 

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

  • 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:

_parse_tag_data(elem_code, elem_num, raw_data)

source code 

Return single data value (PRIVATE).

  • 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]


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


{'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\


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




{'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\