def get_metagene_positions(self):
piece_CDSs, max_gene_length = self.get_CDSs()
read_positions = self.load_read_positions()
metagene_positions = positions.compute_metagene_positions(piece_CDSs,
read_positions,
max_gene_length,
)
self.write_file('metagene_positions', metagene_positions)
three_prime_read_positions = self.load_read_positions(modifier='three_prime')
read_positions = self.load_read_positions(modifier='three_prime')
processed_read_positions = {}
for name, counts in read_positions.iteritems():
gene = {'three_prime_genomic': counts[0],
'three_prime_nongenomic': counts['all'] - counts[0],
'sequence': counts['sequence'],
}
processed_read_positions[name] = gene
three_prime_metagene_positions = positions.compute_metagene_positions(piece_CDSs,
processed_read_positions,
max_gene_length,
)
self.write_file('three_prime_metagene_positions', three_prime_metagene_positions)
def get_metagene_positions(self):
piece_CDSs, max_gene_length = self.get_CDSs()
read_positions = self.load_read_positions()
processed_read_positions = {}
for name in read_positions:
gene = {
'three_prime_genomic':
read_positions[name][0],
'three_prime_nongenomic':
read_positions[name]['all'] - read_positions[name][0],
'three_prime_nonunique':
three_prime_counts['all_nonunique'],
'sequence':
read_positions[name]['sequence'],
}
processed_read_positions[name] = gene
metagene_positions = positions.compute_metagene_positions(
piece_CDSs,
processed_read_positions,
max_gene_length,
)
self.write_file('metagene_positions', metagene_positions)
def get_metagene_positions(self):
piece_CDSs, max_gene_length = self.get_CDSs()
read_positions = self.load_read_positions()
metagene_positions = positions.compute_metagene_positions(piece_CDSs,
read_positions,
max_gene_length,
)
self.write_file('metagene_positions', metagene_positions)
def get_metagene_positions(self):
piece_CDSs, max_gene_length = self.get_CDSs()
read_positions = self.load_read_positions()
processed_read_positions = {}
for name in read_positions:
gene = {'three_prime_genomic': read_positions[name][0],
'three_prime_nongenomic': read_positions[name]['all'] - read_positions[name][0],
'three_prime_nonunique': three_prime_counts['all_nonunique'],
'sequence': read_positions[name]['sequence'],
}
processed_read_positions[name] = gene
metagene_positions = positions.compute_metagene_positions(piece_CDSs,
processed_read_positions,
max_gene_length,
)
self.write_file('metagene_positions', metagene_positions)
