flowcraft/templates/process_viral_assembly.py
def _parse_assembly(self, assembly_file):
        """Parse an assembly fasta file.

        This is a Fasta parsing method that populates the
        :py:attr:`~Assembly.contigs` attribute with data for each contig in the
        assembly.

        The insertion of data on the self.contigs is done by the
        :py:meth:`Assembly._populate_contigs` method, which also calculates
        GC content and proportions.

        Parameters
        ----------
        assembly_file : str
            Path to the assembly fasta file.

        """

        # Temporary storage of sequence data
        seq_temp = []
        # Id counter for contig that will serve as key in self.contigs
        contig_id = 0
        # Initialize kmer coverage and header
        cov, header = None, None

        with open(assembly_file) as fh:

            logger.debug("Starting iteration of assembly file: {}".format(
                assembly_file))
            for line in fh:
                # Skip empty lines
                if not line.strip():
                    continue
                else:
                    # Remove whitespace surrounding line for further processing
                    line = line.strip()

                if line.startswith(">"):
                    # If a sequence has already been populated, save the
                    # previous contig information
                    if seq_temp:
                        # Use join() to convert string list into the full
                        # contig string. This is generally much more efficient
                        # than successively concatenating strings.
                        seq = "".join(seq_temp)

                        logger.debug("Populating contig with contig_id '{}', "
                                     "header '{}' and cov '{}'".format(
                                        contig_id, header, cov))
                        self._populate_contigs(contig_id, header, cov, seq)

                        # Reset temporary sequence storage
                        seq_temp = []
                        contig_id += 1

                    header = line[1:]
                    cov = self._parse_coverage(line)

                else:
                    seq_temp.append(line)

            # Populate last contig entry
            logger.debug("Populating contig with contig_id '{}', "
                         "header '{}' and cov '{}'".format(
                            contig_id, header, cov))
            seq = "".join(seq_temp)
            self._populate_contigs(contig_id, header, cov, seq)
def _parse_assembly(self, assembly_file):
        """Parse an assembly fasta file.

        This is a Fasta parsing method that populates the
        :py:attr:`~Assembly.contigs` attribute with data for each contig in the
        assembly.

        The insertion of data on the self.contigs is done by the
        :py:meth:`Assembly._populate_contigs` method, which also calculates
        GC content and proportions.

        Parameters
        ----------
        assembly_file : str
            Path to the assembly fasta file.

        """

        # Temporary storage of sequence data
        seq_temp = []
        # Id counter for contig that will serve as key in self.contigs
        contig_id = 0
        # Initialize kmer coverage and header
        cov, header = None, None

        with open(assembly_file) as fh:

            logger.debug("Starting iteration of assembly file: {}".format(
                assembly_file))
            for line in fh:
                # Skip empty lines
                if not line.strip():
                    continue
                else:
                    # Remove whitespace surrounding line for further processing
                    line = line.strip()

                if line.startswith(">"):
                    # If a sequence has already been populated, save the
                    # previous contig information
                    if seq_temp:
                        # Use join() to convert string list into the full
                        # contig string. This is generally much more efficient
                        # than successively concatenating strings.
                        seq = "".join(seq_temp)

                        logger.debug("Populating contig with contig_id '{}', "
                                     "header '{}' and cov '{}'".format(
                                        contig_id, header, cov))
                        self._populate_contigs(contig_id, header, cov, seq)

                        # Reset temporary sequence storage
                        seq_temp = []
                        contig_id += 1

                    header = line[1:]
                    cov = self._parse_coverage(line)

                else:
                    seq_temp.append(line)

            # Populate last contig entry
            logger.debug("Populating contig with contig_id '{}', "
                         "header '{}' and cov '{}'".format(
                            contig_id, header, cov))
            seq = "".join(seq_temp)
            self._populate_contigs(contig_id, header, cov, seq)
Parse an assembly fasta file.

        This is a Fasta parsing method that populates the
        :py:attr:`~Assembly.contigs` attribute with data for each contig in the
        assembly.

        The insertion of data on the self.contigs is done by the
        :py:meth:`Assembly._populate_contigs` method, which also calculates
        GC content and proportions.

        Parameters
        ----------
        assembly_file : str
            Path to the assembly fasta file.