###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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"""Convert :term:`ABI` format to :term:`FASTA` format"""
from bioconvert import ConvBase, requires
__all__ = ["ABI2FASTA"]
[docs]class ABI2FASTA(ConvBase):
"""Convert :term:`ABI` file to :term:`FASTQ` file
:term:`ABI` files are created by ABI sequencing machine and includes
PHRED quality scores for base calls. This allows the creation of
:term:`FastA` 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 FASTA filename
"""
super(ABI2FASTA, 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.
:reference: `Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
from Bio import SeqIO
records = SeqIO.parse(self.infile, "abi")
SeqIO.write(records, self.outfile, "fasta")