def compute_codon_occupancy_counts(self):
read_positions = self.load_read_positions()
buffered_codon_counts = {}
codon_counts = {}
codon_counts_stringent = {}
codon_counts_anisomycin = {}
for name, position_counts in read_positions.iteritems():
buffered_counts, identities = positions.compute_codon_counts(position_counts, self.offset_type)
buffered_counts_stringent, _ = positions.compute_codon_counts(position_counts, self.offset_type + '_stringent')
buffered_counts_anisomycin, _ = positions.compute_codon_counts(position_counts, self.offset_type + '_anisomycin')
buffered_codon_counts[name] = {'relaxed': buffered_counts,
'stringent': buffered_counts_stringent,
'anisomycin': buffered_counts_anisomycin,
'identities': identities,
}
num_codons = buffered_counts.CDS_length
# + 1 is to include the stop codon
codon_counts[name] = buffered_counts['start_codon', :num_codons + 1]
codon_counts_stringent[name] = buffered_counts_stringent['start_codon', :num_codons + 1]
codon_counts_anisomycin[name] = buffered_counts_anisomycin['start_codon', :num_codons + 1]
self.write_file('buffered_codon_counts', buffered_codon_counts)
self.write_file('codon_counts', codon_counts)
self.write_file('codon_counts_anisomycin', codon_counts_anisomycin)
self.write_file('codon_counts_stringent', codon_counts_stringent)
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)
