biopython v1.71.0 Bio.SeqIO.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
Link to this section Summary
Iterator for the Abi file format
Iterator for the Abi file format that yields trimmed SeqRecord objects
Generator that returns directory contents
Trims the sequence using Richard Mott’s modified trimming algorithm
Returns single data value
Link to this section Functions
Iterator for the Abi file format.
Iterator for the Abi file format that yields trimmed SeqRecord objects.
Generator that returns directory contents.
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
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