Python Fastq Examples

Example #1

File: Fast5File.py Project: malloryfreeberg/poretools

    def _extract_fastqs_from_fast5(self):
        """
		Return the sequence in the FAST5 file in FASTQ format
		"""
        for id, h5path in fastq_paths[self.version].iteritems():
            try:
                table = self.hdf5file[h5path % self.group]
                fq = formats.Fastq(table['Fastq'][()])
                fq.name += " " + self.filename
                self.fastqs[id] = fq
            except Exception, e:
                pass

Example #2

File: Fast5File_pytables.py Project: tmfarrell/ont_dap

	def _extract_fastqs_from_fast5(self):
		"""
		Return the sequence in the FAST5 file in FASTQ format
		"""
		for id, h5path in fastq_paths.iteritems(): 
			try:
				table = self.hdf5file.getNode(h5path)
				fq = formats.Fastq(table.Fastq[()])
				fq.name += "_" + id + ":" + self.filename
				self.fastqs[id] = fq
			except Exception, e:
				pass