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# Bioconvert is a project to facilitate the interconversion #
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"""Convert :term:`ABI` format to :term:`QUAL` format"""
from bioconvert import ConvBase, requires
__all__ = ["ABI2QUAL"]
[docs]class ABI2QUAL(ConvBase):
"""Convert :term:`ABI` file to :term:`QUAL` file
:term:`ABI` files are created by ABI sequencing machine and
includes PHRED quality scores for base calls. This allows
the creation of :term:`QUAL` files.
Method implemented is based on BioPython [BIOPYTHON]_.
"""
#: Default value
_default_method = "biopython"
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input ABI file
:param str outfile: output QUAL filename
"""
super(ABI2QUAL, self).__init__(infile, outfile, *args, **kargs)
[docs] @requires(python_library="biopython")
def _method_biopython(self, *args, **kwargs):
"""For this method we use the biopython package Bio.SeqIO.
`Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
from Bio import SeqIO
records = SeqIO.parse(self.infile, "abi")
# output using SeqIO.write(records, self.outfile, "qual") is not
# standard so we write our own conversion here below
with open(self.outfile, "w") as fout:
for rec in records:
header = rec.name
qual = rec.letter_annotations["phred_quality"]
qual = "".join([str(x) for x in qual])
fout.write(">{}\n".format(header))
fout.write("{}\n".format(qual))