forked from morgonfrilla/PyClone
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trace.py
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trace.py
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'''
Created on 2013-04-23
@author: Andrew Roth
'''
import bz2
import csv
import os
from utility import make_directory
class DiskTrace(object):
def __init__(self, trace_dir, sample_ids, mutation_ids, attribute_map, precision=False):
self.trace_dir = trace_dir
self.sample_ids = sample_ids
self.mutation_ids = mutation_ids
self.attribute_map = attribute_map
self.update_precision = precision
def close(self):
self.alpha_writer.close()
self.labels_writer.close()
for writer in self.cellular_frequency_writers.values():
writer.close()
if self.update_precision:
self.precision_writer.close()
def open(self):
make_directory(self.trace_dir)
self.alpha_writer = ConcentrationParameterWriter(self.trace_dir)
self.labels_writer = LabelsWriter(self.trace_dir, self.mutation_ids)
self.cellular_frequency_writers = {}
for sample_id in self.sample_ids:
self.cellular_frequency_writers[sample_id] = CellularFrequenciesWriter(self.trace_dir,
sample_id,
self.mutation_ids)
if self.update_precision:
self.precision_writer = PrecisionWriter(self.trace_dir)
def update(self, state):
self.alpha_writer.write_row([state['alpha'], ])
self.labels_writer.write_row(state['labels'])
for sample_id in self.sample_ids:
row = []
for param in state['params']:
attr = self.attribute_map['cellular_frequencies']
row.append(getattr(param[sample_id], attr))
self.cellular_frequency_writers[sample_id].write_row(row)
if self.update_precision:
self.precision_writer.write_row([state['global_params'].x])
class ConcentrationParameterWriter(object):
def __init__(self, trace_dir):
self.file_name = os.path.join(trace_dir, 'alpha.tsv.bz2')
self.file_handle = bz2.BZ2File(self.file_name, 'w')
self.writer = csv.writer(self.file_handle, delimiter='\t')
self.param_id = 'alpha'
def close(self):
self.file_handle.close()
def write_row(self, row):
self.writer.writerow(row)
class CellularFrequenciesWriter(object):
def __init__(self, trace_dir, sample_id, mutation_ids):
self.file_name = os.path.join(trace_dir, '{0}.cellular_prevalence.tsv.bz2'.format(sample_id))
self.file_handle = bz2.BZ2File(self.file_name, 'w')
self.writer = csv.writer(self.file_handle, delimiter='\t')
self.writer.writerow(mutation_ids)
self.param_id = (sample_id, 'cellular_frequencies')
def close(self):
self.file_handle.close()
def write_row(self, row):
self.writer.writerow(row)
class LabelsWriter(object):
def __init__(self, trace_dir, mutation_ids):
self.file_name = os.path.join(trace_dir, 'labels.tsv.bz2')
self.file_handle = bz2.BZ2File(self.file_name, 'w')
self.writer = csv.writer(self.file_handle, delimiter='\t')
self.writer.writerow(mutation_ids)
self.param_id = 'labels'
def close(self):
self.file_handle.close()
def write_row(self, row):
self.writer.writerow(row)
class PrecisionWriter(object):
def __init__(self, trace_dir):
self.file_name = os.path.join(trace_dir, 'precision.tsv.bz2')
self.file_handle = bz2.BZ2File(self.file_name, 'w')
self.writer = csv.writer(self.file_handle, delimiter='\t')
self.param_id = 'precision'
def close(self):
self.file_handle.close()
def write_row(self, row):
self.writer.writerow(row)