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ericmjl / protein-systematic-characterization

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Accessing ABI chromatogram data #27

Closed ericmjl closed 7 years ago

ericmjl commented 7 years ago

Putting this here for record - should be helpful for analyzing traces of sequencing data.

Hi Eric,

I think you want the raw DATA1, DATA2, DATA3 and DATA4 values (for the four bases) which are exposed via the Biopython ABI parser, e.g.

from Bio import SeqIO record = SeqIO.read("310.ab1", "abi") print(record.annotations['abif_raw']['DATA1'])

See also http://www.appliedbiosystem.com/support/software_community/ABIF_File_Format.pdf

Peter

ericmjl commented 7 years ago

I have a recipe put up on the BioPython website now. Reference: http://biopython.org/wiki/ABI_traces