Python Genome.import_fasta_file Examples

Example #1

File: convert_external_genome.py Project: nate-d-olson/NASP

def main():
    from nasp_objects import Genome, GenomeMeta
    commandline_args = _parse_args()
    external_nickname = commandline_args.name if commandline_args.name else GenomeMeta.generate_nickname_from_filename( commandline_args.external )
    external_genome = Genome()
    external_genome.import_fasta_file( commandline_args.external )
    generate_delta_file( commandline_args.nucmerpath, commandline_args.nucmerargs, commandline_args.deltafilterpath, external_nickname, commandline_args.reference, commandline_args.external )
    franken_genome = Genome()
    parse_delta_file( ( external_nickname + ".filtered.delta" ), franken_genome, external_genome )
    franken_genome.write_to_fasta_file( external_nickname + ".frankenfasta", "franken::" )

Example #2

File: format_fasta.py Project: nate-d-olson/NASP

def main():
    from nasp_objects import Genome
    commandline_args = _parse_args()
    fasta_data = Genome()
    fasta_data.import_fasta_file( commandline_args.inputfasta )
    fasta_data.write_to_fasta_file( commandline_args.outputfasta )