Package Bio :: Package SeqIO :: Module AbiIO

Module AbiIO

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

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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

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_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'

Function Details

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_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',
...