###########################################################################
# 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. #
# #
# bioconvert is free software: you can redistribute it and/or modify #
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# bioconvert is distributed in the hope that it will be useful, #
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# along with this program (COPYING file). #
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# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Convert :term:`FASTA` format to :term:`FASTQ` format"""
import sys
import colorlog
from bioconvert import ConvBase
from bioconvert.core.base import ConvArg
from bioconvert.core.decorators import requires
from bioconvert.core.extensions import extensions
_log = colorlog.getLogger(__name__)
[docs]class FASTA_QUAL2FASTQ(ConvBase):
"""Convert FASTA and QUAL back into a FASTQ file
Method based on pysam [PYSAM]_.
"""
#: Default value
_default_method = "pysam"
def __init__(self, infile, outfile):
"""
:param list infile: The path to the input FASTA file, the path to the input QUAL file
:param str outfile: The path to the output FASTQ file
"""
super(FASTA_QUAL2FASTQ, self).__init__(infile, outfile)
[docs] @requires(python_library="pysam")
def _method_pysam(self, *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 self.infile[1] is None:
_log.error("No quality file provided. Please add a quality file path ")
sys.exit(1)
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[0]), FastxFile(self.infile[1])):
assert seq.name == qual.name
if seq.comment:
fastq_out.write(
"@{0} {1}\n{2}\n+\n{3}\n".format(seq.name, seq.comment, seq.sequence, qual.sequence)
)
else:
fastq_out.write("@{0}\n{1}\n+\n{2}\n".format(seq.name, seq.sequence, qual.sequence))
@staticmethod
def get_IO_arguments():
yield ConvArg(
names="input_file",
nargs=2,
default=None,
type=ConvArg.file,
help="The path to the file to convert.",
)
yield ConvArg(
names="output_file",
default=None,
type=ConvArg.file,
output_argument=True,
help="The path where the result will be stored.",
)