###########################################################################
# 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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# #
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# GNU General Public License for more details. #
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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:`SCF` file to :term:`FASTQ` file"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires_nothing
from bioconvert.io import scf
_log = colorlog.getLogger(__name__)
__all__ = ["SCF2FASTQ"]
[docs]class SCF2FASTQ(ConvBase):
"""
Converts a binary :term:`SCF` file to :term:`FastQ` file
:param str infile: input SCF file
:param str outfile: output name file
"""
#: Default value
_default_method = "python"
[docs] @requires_nothing
@compressor
def _method_python(self, *args, **kwargs):
"""Internal method"""
sequence, qualities, comments = scf.read_scf(self.infile)
# Wrinting output file
with open(self.outfile, "w") as output_file:
output_file.write("@" + comments.replace("\n", "-").replace(" ", "_") + "\n")
output_file.write(sequence + "\n")
output_file.write("+" + comments.replace("\n", "-").replace(" ", "_") + "\n")
for i in qualities:
if i > 92:
output_file.write(chr(126))
else:
output_file.write(chr(i + 34))
output_file.write("\n")
"""
print(sequence)
print("INFORMATIONS")
print("magic_number = " + magic_number.decode("utf-8"))
print("samples = " + str(samples))
print("samples_offset = " + str(samples_offset))
print("bases = " + str(bases))
print("bases_left_clip = " + str(bases_left_clip))
print("bases_right_clip = " + str(bases_right_clip))
print("bases_offset = " + str(bases_offset))
print("comments_size = " + str(comments_size))
print("comments_offset = " + str(comments_offset))
print("version = " + version.decode("utf-8"))
print("sample_size = " + str(sample_size))
print("code_set = " + str(code_set))
print("private_size = " + str(private_size))
print("private_offset = " + str(private_offset))
#print("spare = " + str(spare))
print()
print("COMMENTS")
print(comments)
print()
print("SEQUENCE")
print(sequence)
print()
print("QUALITIES")
print(qualities)
"""
"""
http://staden.sourceforge.net/manual/formats_unix_2.html
http://doc.bioperl.org/bioperl-live/Bio/SeqIO/scf.html#POD6
https://docs.python.org/2/library/struct.html
http://www.perlmonks.org/?node_id=224666
SCF file organisation (more or less)
Length in bytes Data
---------------------------------------------------------------------------
128 header
Number of samples * sample size Samples for A trace
Number of samples * sample size Samples for C trace
Number of samples * sample size Samples for G trace
Number of samples * sample size Samples for T trace
Number of bases * 4 Offset into peak index for each base
Number of bases Accuracy estimate bases being 'A'
Number of bases Accuracy estimate bases being 'C'
Number of bases Accuracy estimate bases being 'G'
Number of bases Accuracy estimate bases being 'T'
Number of bases The called bases
Number of bases * 3 Reserved for future use
Comments size Comments
Private data size Private data
"""