from Bio import SeqIO import argparse import sys, os sys.path.insert(0, str(os.path.dirname(os.path.realpath(__file__))) + "/../") from database.genomedb import GenomeDB if __name__ == '__main__': parser = argparse.ArgumentParser( description='Calculate kmer histograms and compare for two groups', add_help=False) parser.add_argument('-l', '--location', type=str, help='input', required=True) args = parser.parse_args() fileLocation = args.location for file in glob.glob(fileLocation + '/*.gb'): print(file) genomeDB = GenomeDB(fileLocation, loadAll=False) genomeDB.loadGenome(file, False) genomeDB.writeBLASTfastas(fileLocation)
from analysis.homologybuilder import HomologyBuilder from database.genomedb import GenomeDB if __name__ == '__main__': fileLocation = '/mnt/c/ownCloud/data/cbdb/' initialise=False if initialise: genomDB = GenomeDB(fileLocation + "genomes/", fileFormat='gb', fileExtension='.gbff', loadAll=True) genomDB.writeBLASTfastas(fileLocation + "genomes/") exit() builder = HomologyBuilder(basePath=fileLocation, inputFormat='gb', inputExtension='.gbff') homolDB = builder.analyse() homolDB.save_to_file(fileLocation + "/cbj")