def extract(self):
# Call extraction #
shell_output('sffinfo -s %s > %s' % (self.p.raw_sff, self.p.raw_fasta))
shell_output('sffinfo -q %s > %s' % (self.p.raw_sff, self.p.raw_qual))
shell_output('sffinfo -m %s > %s' % (self.p.raw_sff, self.p.manifest))
# Convert #
sh.fasta_to_fastq(self.p.raw_fasta, self.p.raw_qual, self.p.raw_fastq)
def extract(self):
# Call extraction #
shell_output('sffinfo -s %s > %s' % (self.p.raw_sff, self.p.raw_fasta))
shell_output('sffinfo -q %s > %s' % (self.p.raw_sff, self.p.raw_qual))
shell_output('sffinfo -m %s > %s' % (self.p.raw_sff, self.p.manifest))
# Convert #
sh.fasta_to_fastq(self.p.raw_fasta, self.p.raw_qual, self.p.raw_fastq)
def raw(self):
# Call extraction #
shell_output('sffinfo -s %s > %s' % (self.p.raw_sff, self.p.raw_fasta))
shell_output('sffinfo -q %s > %s' % (self.p.raw_sff, self.p.raw_qual))
shell_output('sffinfo -m %s > %s' % (self.p.raw_sff, self.p.manifest))
# Convert #
sh.fasta_to_fastq(self.p.raw_fasta, self.p.raw_qual, self.p.raw_fastq)
# Fast QC #
sh.fastqc(self.p.raw_fastq, '-o', self.p.raw_dir, '-q')
if os.path.exists(self.p.raw_dir + 'raw_fastqc.zip'): os.remove(self.p.raw_dir + 'raw_fastqc.zip')
def no_barcode_split(self):
"""Will translate the SFF files without barcodes. Just to explore an SFF file."""
shell_output('sffinfo -s %s > %s' % (self.path, self.raw_fasta_path))
shell_output('sffinfo -q %s > %s' % (self.path, self.raw_qual_path))
sh.fasta_to_fastq(self.raw_fasta_path, self.raw_qual_path, self.fastq)
def no_barcode_split(self):
"""Will translate the SFF files without barcodes. Just to explore an SFF file."""
shell_output('sffinfo -s %s > %s' % (self.path, self.raw_fasta_path))
shell_output('sffinfo -q %s > %s' % (self.path, self.raw_qual_path))
sh.fasta_to_fastq(self.raw_fasta_path, self.raw_qual_path, self.fastq)
