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)