flowcraft/templates/megahit.py
def fix_contig_names(asseembly_path):
    """Removes whitespace from the assembly contig names

    Parameters
    ----------
    asseembly_path : path to assembly file

    Returns
    -------
    str:
        Path to new assembly file with fixed contig names
    """

    fixed_assembly = "fixed_assembly.fa"

    with open(asseembly_path) as in_hf, open(fixed_assembly, "w") as ou_fh:

        for line in in_hf:

            if line.startswith(">"):
                fixed_line = line.replace(" ", "_")
                ou_fh.write(fixed_line)
            else:
                ou_fh.write(line)

    return fixed_assembly
def fix_contig_names(asseembly_path):
    """Removes whitespace from the assembly contig names

    Parameters
    ----------
    asseembly_path : path to assembly file

    Returns
    -------
    str:
        Path to new assembly file with fixed contig names
    """

    fixed_assembly = "fixed_assembly.fa"

    with open(asseembly_path) as in_hf, open(fixed_assembly, "w") as ou_fh:

        for line in in_hf:

            if line.startswith(">"):
                fixed_line = line.replace(" ", "_")
                ou_fh.write(fixed_line)
            else:
                ou_fh.write(line)

    return fixed_assembly
Removes whitespace from the assembly contig names

    Parameters
    ----------
    asseembly_path : path to assembly file

    Returns
    -------
    str:
        Path to new assembly file with fixed contig names