def get_mutation_rep_time(mutation_file, sample_name):
""" Returns list with replication timings of mutated nucleotides
with given sample name, mutation motif and final nucleotide"""
sys.stdout.write("\nConsidering {0} sample: ".format(sample_name))
mutation_rep_time = []
# We consider chromosomes separately to avoid memory overflow:
# All genome in str format ~ 3.1 GB - too much for RAM in my PC
genome_file_names = core.get_genome_file_names()
for chromosome in genome_file_names:
sys.stdout.write(chromosome + ', ')
sys.stdout.flush()
mutations_list = core.read_mutations(mutation_file,
mutation_type='subs',
chromosome=chromosome,
sample_names=[sample_name],
final_nucleotides=core.FINAL_NUCL)
with open(genome_file_names[chromosome]) as genome_file:
genom = genome_file.read()
for index, mutation in mutations_list.iterrows():
# FIXME: Considering mutations_list 20 times - unefficient
position = mutation['positionFrom']
motif = genome[position - 2: position + 1]
if motif in core.MOTIFS:
rep_time = core.calculate_replication_timing(chromosome,
position)
if rep_time == -1:
print '\nuncalculatable replication time at\
{0}:{1}'.format(chromosome, position)
mutation_rep_time.append(rep_time)
del genome
return mutation_rep_time
def filterMutations(mutations_file, catalogFileName, out_file):
""" in: file with mutations; catalog with list of genome samples
out: writes all mutations (exclude indel mutations and exome samples)
to out file, specified by out_file; returns nothing """
genomeSampleNames = [] # all samples except exome samples
with open(catalogFileName) as catalogFile:
genomeSampleNames = catalogFile.readline()[:-1].split('\t')
genomeSampleNames.pop(0) # First and second words are "Mutation type"
mutations = core.read_mutations(mutations_file, mutation_type='subs',
sample_names=genomeSampleNames)
mutations.to_csv(out_file, sep='\t', header=False, index=False)
return
def check_chromosome(genome_file, mutations_file, chromosome):
"""Checks is (initialNucleotide, position) in mutations_file
placed according to genome_file"""
with open(genome_file, 'r') as f:
genome_sequence = f.read()
mutations_list = core.read_mutations(mutations_file,
mutation_type='subs',
chromosome=chromosome)
for index, mutation in mutations_list.iterrows():
position = mutation['positionFrom']
genome_nucleotide = genome_sequence[position - 1]
mutation_nucleotide = mutation['initialNucl']
if genome_nucleotide != mutation_nucleotide:
message = '\n{0}:{1} nucleotide in genome ({2}) and\
mutations file ({3}) not equal'
sys.exit(message.format(chromosome, position,
genome_nucleotide,
mutation_nucleotide))
print "Chromosome {0} check succeed".format(chromosome)
return