def _anonymize_pooled_gsa(
self, file_path_output_pooled_anonymous, sequence_prefix):
"""
Anonymize assembly of a sample.
@param file_path_output_pooled_anonymous: file paths of assembly from all samples
@type file_path_output_pooled_anonymous: str | unicode
@param sequence_prefix: Prefix for anonymous sequence names
@type sequence_prefix: str | unicode
@return: File path of anonymized assembly and file path of a sequence name mapping
@rtype: tuple[str|unicode, str|unicode]
"""
fastaanonymizer = FastaAnonymizer(
logfile=self._logfile,
verbose=self._verbose,
debug=self._debug,
seed=None,
tmp_dir=self._project_file_folder_handler.get_tmp_wd()
)
file_path_output_anonymous, file_path_anonymous_mapping = fastaanonymizer.shuffle_anonymize(
path_input=file_path_output_pooled_anonymous,
prefix=sequence_prefix,
file_format="fasta")
return file_path_output_anonymous, file_path_anonymous_mapping
def _anonymize_reads(self, directory_fastq, sequence_prefix, paired_end):
"""
Anonymize simulated reads.
@param directory_fastq: fastq directory of a sample
@type directory_fastq: str | unicode
@param sequence_prefix: Prefix for anonymous sequence names
@type sequence_prefix: str | unicode
@param paired_end: True if reads are paired
@type paired_end: bool
@return: File path of anonymized reads and file path of a sequence name mapping
@rtype: tuple[str|unicode, str|unicode]
"""
fastaanonymizer = FastaAnonymizer(
logfile=self._logfile,
verbose=self._verbose,
debug=self._debug,
seed=None,
tmp_dir=self._project_file_folder_handler.get_tmp_wd()
)
if paired_end:
file_path_output_anonymous_reads, file_path_anonymous_mapping = fastaanonymizer.interweave_shuffle_anonymize(
directory_fastq,
prefix=sequence_prefix,
file_format="fastq",
file_extension="fq")
else:
file_path_output_anonymous_reads, file_path_anonymous_mapping = fastaanonymizer.shuffle_anonymize(
directory_fastq,
prefix=sequence_prefix,
file_format="fastq",
file_extension="fq")
return file_path_output_anonymous_reads, file_path_anonymous_mapping