flowcraft/templates/process_viral_assembly.py
def _populate_contigs(self, contig_id, header, cov, sequence):
        """ Inserts data from a single contig into\
         :py:attr:`~Assembly.contigs`.

        By providing a contig id, the original header, the coverage that
        is parsed from the header and the sequence, this method will
        populate the :py:attr:`~Assembly.contigs` attribute.

        Parameters
        ----------
        contig_id : int
            Arbitrary unique contig identifier.
        header : str
            Original header of the current contig.
        cov : float
            The contig coverage, parsed from the fasta header
        sequence : str
            The complete sequence of the contig.

        """

        # Get AT/GC/N counts and proportions.
        # Note that self._get_gc_content returns a dictionary with the
        # information on the GC/AT/N counts and proportions. This makes it
        # much easier to add to the contigs attribute using the ** notation.
        gc_kwargs = self._get_gc_content(sequence, len(sequence))
        logger.debug("Populate GC content with: {}".format(gc_kwargs))

        self.contigs[contig_id] = {
            "header": header,
            "sequence": sequence,
            "length": len(sequence),
            "kmer_cov": cov,
            **gc_kwargs
        }
def _populate_contigs(self, contig_id, header, cov, sequence):
        """ Inserts data from a single contig into\
         :py:attr:`~Assembly.contigs`.

        By providing a contig id, the original header, the coverage that
        is parsed from the header and the sequence, this method will
        populate the :py:attr:`~Assembly.contigs` attribute.

        Parameters
        ----------
        contig_id : int
            Arbitrary unique contig identifier.
        header : str
            Original header of the current contig.
        cov : float
            The contig coverage, parsed from the fasta header
        sequence : str
            The complete sequence of the contig.

        """

        # Get AT/GC/N counts and proportions.
        # Note that self._get_gc_content returns a dictionary with the
        # information on the GC/AT/N counts and proportions. This makes it
        # much easier to add to the contigs attribute using the ** notation.
        gc_kwargs = self._get_gc_content(sequence, len(sequence))
        logger.debug("Populate GC content with: {}".format(gc_kwargs))

        self.contigs[contig_id] = {
            "header": header,
            "sequence": sequence,
            "length": len(sequence),
            "kmer_cov": cov,
            **gc_kwargs
        }
def _populate_contigs ( self , contig_id , header , cov , sequence ) : # Get AT/GC/N counts and proportions. # Note that self._get_gc_content returns a dictionary with the # information on the GC/AT/N counts and proportions. This makes it # much easier to add to the contigs attribute using the ** notation. gc_kwargs = self . _get_gc_content ( sequence , len ( sequence ) ) logger . debug ( "Populate GC content with: {}" . format ( gc_kwargs ) ) self . contigs [ contig_id ] = { "header" : header , "sequence" : sequence , "length" : len ( sequence ) , "kmer_cov" : cov , * * gc_kwargs }
Inserts data from a single contig into\
         :py:attr:`~Assembly.contigs`.

        By providing a contig id, the original header, the coverage that
        is parsed from the header and the sequence, this method will
        populate the :py:attr:`~Assembly.contigs` attribute.

        Parameters
        ----------
        contig_id : int
            Arbitrary unique contig identifier.
        header : str
            Original header of the current contig.
        cov : float
            The contig coverage, parsed from the fasta header
        sequence : str
            The complete sequence of the contig.
Inserts data from a single contig into \ : py : attr : ~Assembly . contigs .