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")