###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
# #
# Copyright © 2018-2022 Institut Pasteur, Paris and CNRS. #
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"""Convert :term:`FASTA` format to :term:`FASTQ` format"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["FASTA2FASTQ"]
[docs]class FASTA2FASTQ(ConvBase):
"""
Methods available are based on pysam [PYSAM]_.
"""
#: Default value
_default_method = "pysam"
def __init__(self, infile, outfile):
"""
:param str infile: The path to the input FASTA file
:param str outfile: The path to the output FASTQ file
"""
super(FASTA2FASTQ, self).__init__(infile, outfile)
[docs] @requires(python_library="pysam")
@compressor
def _method_pysam(self, quality_file=None, *args, **kwargs):
"""This method uses the FastxFile function of the Pysam python module.
`FastxFile documentation <https://pysam.readthedocs.io/en/latest/api.html#pysam.FastxFile.close>`_"""
from pysam import FastxFile
if quality_file is None:
_log.warning("No quality file provided. Please use --quality-file")
with open(self.outfile, "w") as fastq_out:
for seq in FastxFile(self.infile):
fastq_out.write(
"@{0} {1}\n{2}\n+\n{3}\n".format(seq.name, seq.comment, seq.sequence, len(seq.sequence) * "I")
)
else: # length must be equal and identifiers sorted similarly
with open(self.outfile, "w") as fastq_out:
for seq, qual in zip(FastxFile(self.infile), FastxFile(quality_file)):
assert seq.name == qual.name
fastq_out.write(
"@{0} {1}\n{2}\n+\n{3}\n".format(seq.name, seq.comment, seq.sequence, qual.sequence)
)