sequences2 = util.get_sequences(file2)
data, labels = create_data(sequences1, sequences2)
return data, labels
# pipeline
if __name__ == '__main__':
print("Python version:\n{}\n".format(sys.version))
print("matplotlib version: {}".format(matplotlib.__version__))
print(plt.style.available)
print("numpy version: {}".format(np.__version__))
input_file = sys.argv[1]
output_dir = sys.argv[2]
util.remove_old_output_files(output_dir)
sys.stdout = open(util.generate_output_filename(output_dir), "w")
lines = util.readFile(input_file)
threegrams = create_keys(3)
twograms = create_keys(2)
proteins = []
accuracies = []
for line in lines:
if line:
print("-----------------------------------------")
print(line[0], line[1], line[2], line[3])
print("start processing ", line[2], line[3])
file1 = line[0]
file2 = line[1]
analysis_type = line[2]
protein = line[3]
util.start_roc_plot(analysis_type + '-' + protein)
def get_m1_m2_sequences(fasta_file):
m1_sequences = [x.seq for x in SeqIO.parse(fasta_file, "fasta") if len(x.description.split("|"))>3 and x.description.split("|")[3].split(":")[1]=='M1']
m2_sequences = [x.seq for x in SeqIO.parse(fasta_file, "fasta") if len(x.description.split("|"))>3 and x.description.split("|")[3].split(":")[1]=='M2']
return m1_sequences, m2_sequences
def readFile(filename):
f = open(filename)
csv_f = csv.reader(f)
return csv_f
#pipeline
if __name__ == '__main__':
input_file = sys.argv[1]
output_dir = sys.argv[2]
util.remove_old_output_files(output_dir)
sys.stdout = open(util.generate_output_filename(output_dir, basename='dna_results'), "w")
lines = util.readFile(input_file)
threegrams = create_keys(3)
proteins = []
accuracies = []
for line in lines:
if line:
print("-----------------------------------------")
print(line[0], line[1], line[2], line[3])
print("start processing ", line[2], line[3])
file1 = line[0]
file2 = line[1]
analysis_type = line[2]
protein = line[3]