def get_event_data_as_stream(self, event_name):
"""
Get data for given event. If there's no data, return None.
"""
# The name of the event as stored in database (if using
# compressed event IDs, this would be a misocomp ID)
event_to_query = event_name
# Error checking: if the database is compressed but we're not
# given a mapping, this is a major error
if self.is_db_events_compressed and \
((self.comp_to_uncomp is None) or (self.uncomp_to_comp is None)):
raise Exception, "The database contains compressed IDs but no " \
"mapping (.shelve) file was given."
# If we have a compressed event representation in database and
# the event given is uncompressed, then look at the
# compressed representation
if self.is_db_events_compressed and \
(not misc_utils.is_compressed_name(event_name)):
if event_name not in self.uncomp_to_comp:
return None
event_to_query = self.uncomp_to_comp[event_name]
# If the event given is compressed and the database representation
# is *uncompressed*, then uncompress the event
elif (not self.is_db_events_compressed) and \
misc_utils.is_compressed_name(event_name):
# If there's no compressed mapping, we can't
# use this event
if self.comp_to_uncomp is None:
raise Exception, "Cannot get compressed event %s from " \
"uncompressed database." %(event_name)
if event_name not in self.comp_to_uncomp:
return None
event_to_query = self.comp_to_uncomp[event_name]
c = self.conn.cursor()
results = \
c.execute("SELECT * from %s WHERE event_name=\'%s\'" \
%(self.table_name,
event_to_query))
rows = results.fetchall()
if len(rows) == 0:
# Event not found
return None
if len(rows) > 1:
raise Exception, \
"More than one entry for event %s" %(event_to_query)
event_name, psi_vals_and_scores, header = rows[0]
# If we're given a mapping to compressed events,
# return the event name as the *uncompressed* event
# name
event_data = "%s\n%s\n" %(header,
psi_vals_and_scores)
event_stream = StringIO.StringIO(event_data)
return event_stream
def get_event_data_as_stream(self, event_name):
"""
Get data for given event. If there's no data, return None.
"""
# The name of the event as stored in database (if using
# compressed event IDs, this would be a misocomp ID)
event_to_query = event_name
# Error checking: if the database is compressed but we're not
# given a mapping, this is a major error
if self.is_db_events_compressed and \
((self.comp_to_uncomp is None) or (self.uncomp_to_comp is None)):
raise Exception, "The database contains compressed IDs but no " \
"mapping (.shelve) file was given."
# If we have a compressed event representation in database and
# the event given is uncompressed, then look at the
# compressed representation
if self.is_db_events_compressed and \
(not misc_utils.is_compressed_name(event_name)):
if event_name not in self.uncomp_to_comp:
return None
event_to_query = self.uncomp_to_comp[event_name]
# If the event given is compressed and the database representation
# is *uncompressed*, then uncompress the event
elif (not self.is_db_events_compressed) and \
misc_utils.is_compressed_name(event_name):
# If there's no compressed mapping, we can't
# use this event
if self.comp_to_uncomp is None:
raise Exception, "Cannot get compressed event %s from " \
"uncompressed database." %(event_name)
if event_name not in self.comp_to_uncomp:
return None
event_to_query = self.comp_to_uncomp[event_name]
c = self.conn.cursor()
results = \
c.execute("SELECT * from %s WHERE event_name=\'%s\'" \
%(self.table_name,
event_to_query))
rows = results.fetchall()
if len(rows) == 0:
# Event not found
return None
if len(rows) > 1:
raise Exception, \
"More than one entry for event %s" %(event_to_query)
event_name, psi_vals_and_scores, header = rows[0]
# If we're given a mapping to compressed events,
# return the event name as the *uncompressed* event
# name
event_data = "%s\n%s\n" % (header, psi_vals_and_scores)
event_stream = StringIO.StringIO(event_data)
return event_stream
def is_event_name_compressed(self):
"""
Determine if the events in the database are compressed
or not.
"""
c = self.conn.cursor()
results = \
c.execute("SELECT * from %s" %(self.table_name))
first_result = results.fetchone()
event_name = str(first_result[0])
is_comp = misc_utils.is_compressed_name(event_name)
return is_comp
def is_event_name_compressed(self):
"""
Determine if the events in the database are compressed
or not.
"""
c = self.conn.cursor()
results = \
c.execute("SELECT * from %s" %(self.table_name))
first_result = results.fetchone()
event_name = str(first_result[0])
is_comp = misc_utils.is_compressed_name(event_name)
return is_comp
def get_all_event_names(self):
"""
Return all event names in current samples dir.
"""
all_event_names = []
for curr_fname in self.all_filenames:
if curr_fname.endswith(".miso"):
# It's a regular .miso plain text file
event_name = \
get_event_name(curr_fname,
use_compressed_map=self.compressed_ids_to_genes)
# Record event name and its mapping to a .miso file
all_event_names.append(event_name)
self.event_names_to_fnames[event_name] = curr_fname
elif miso_db.is_miso_db_fname(curr_fname):
# It's a MISO database file, so load all the event
# names in that file
curr_db = \
miso_db.MISODatabase(curr_fname,
comp_to_uncomp=self.compressed_ids_to_genes)
# Record event name and its mapping to the chromosome's
# .miso_db file
for curr_event_name in curr_db.get_all_event_names():
curr_event_name = str(curr_event_name)
event_name_to_use = curr_event_name
# If we're given a mapping of compressed IDs, use the
# mapping to get the uncompressed event name
if self.compressed_ids_to_genes is not None:
# The internal database representation of compressed
# index databases are compressed IDs, so if the
# ID is uncompressed it must be converted to a
# compressed one.
if not misc_utils.is_compressed_name(curr_event_name):
event_name_to_use = \
str(curr_db.uncomp_to_comp[curr_event_name])
all_event_names.append(event_name_to_use)
self.event_names_to_fnames[event_name_to_use] = curr_fname
return all_event_names
def get_all_event_names(self):
"""
Return all event names in current samples dir.
"""
all_event_names = []
for curr_fname in self.all_filenames:
if curr_fname.endswith(".miso"):
# It's a regular .miso plain text file
event_name = \
get_event_name(curr_fname,
use_compressed_map=self.compressed_ids_to_genes)
# Record event name and its mapping to a .miso file
all_event_names.append(event_name)
self.event_names_to_fnames[event_name] = curr_fname
elif miso_db.is_miso_db_fname(curr_fname):
# It's a MISO database file, so load all the event
# names in that file
curr_db = \
miso_db.MISODatabase(curr_fname,
comp_to_uncomp=self.compressed_ids_to_genes)
# Record event name and its mapping to the chromosome's
# .miso_db file
for curr_event_name in curr_db.get_all_event_names():
curr_event_name = str(curr_event_name)
event_name_to_use = curr_event_name
# If we're given a mapping of compressed IDs, use the
# mapping to get the uncompressed event name
if self.compressed_ids_to_genes is not None:
# The internal database representation of compressed
# index databases are compressed IDs, so if the
# ID is uncompressed it must be converted to a
# compressed one.
if not misc_utils.is_compressed_name(curr_event_name):
event_name_to_use = \
str(curr_db.uncomp_to_comp[curr_event_name])
all_event_names.append(event_name_to_use)
self.event_names_to_fnames[event_name_to_use] = curr_fname
return all_event_names
def summarize_sampler_results(samples_dir,
summary_filename,
use_compressed=None):
"""
Given a set of samples from MISO, output a summary file.
"""
summary_file = open(summary_filename, 'w')
header_fields = [
"event_name",
"miso_posterior_mean",
"ci_low",
"ci_high",
"isoforms",
"counts",
"assigned_counts",
# Fields related to gene/event
"chrom",
"strand",
"mRNA_starts",
"mRNA_ends"
]
summary_header = "%s\n" % ("\t".join(header_fields))
summary_file.write(summary_header)
print "Loading events from: %s" % (samples_dir)
print "Writing summary to: %s" % (summary_filename)
samples_obj = MISOSamples(samples_dir, use_compressed=use_compressed)
num_events = 0
for event_name in samples_obj.all_event_names:
samples_results = samples_obj.get_event_samples(event_name)
if samples_results is None:
print "WARNING: Skipping %s" % (event_name)
# Skip files that could not be parsed
continue
# If we're not given a mapping to compressed IDs, check
# that the event IDs do not look compressed
if misc_utils.is_compressed_name(event_name) and \
(use_compressed is None):
print "WARNING: %s looks like a compressed id, but no mapping file " \
"from compressed IDs to event IDs was given! Try: --use-compressed" \
%(event_name)
# Load header/parameters information
samples = samples_results[0]
header = samples_results[1]
header = header[0]
params = parse_sampler_params_from_header(header)
# Get counts information from header
counts_info = samples_results[5]
shape_len = len(shape(samples))
if shape_len < 2:
print "WARNING: Skipping %s -- mishaped file" % (event_name)
continue
num_samples, num_isoforms = shape(samples)
output_fields = format_credible_intervals(event_name, samples)
# Add isoforms information to output fields
isoforms_field = get_isoforms_from_header(header)
output_fields.append(isoforms_field)
# Add counts information to output fields
output_fields.append(counts_info['counts'])
output_fields.append(counts_info['assigned_counts'])
gene_info = get_gene_info_from_params(params)
output_fields.append(gene_info["chrom"])
output_fields.append(gene_info["strand"])
output_fields.append(gene_info["mRNA_starts"])
output_fields.append(gene_info["mRNA_ends"])
output_line = "%s\n" % ("\t".join(output_fields))
summary_file.write(output_line)
num_events += 1
print " - Summarized a total of %d events." % (num_events)
summary_file.close()
def summarize_sampler_results(samples_dir, summary_filename,
use_compressed=None):
"""
Given a set of samples from MISO, output a summary file.
"""
summary_file = open(summary_filename, 'w')
header_fields = ["event_name", "miso_posterior_mean", "ci_low", "ci_high",
"isoforms", "counts", "assigned_counts",
# Fields related to gene/event
"chrom",
"strand",
"mRNA_starts",
"mRNA_ends"]
summary_header = "%s\n" %("\t".join(header_fields))
summary_file.write(summary_header)
print "Loading events from: %s" %(samples_dir)
print "Writing summary to: %s" %(summary_filename)
samples_obj = MISOSamples(samples_dir,
use_compressed=use_compressed)
num_events = 0
for event_name in samples_obj.all_event_names:
samples_results = samples_obj.get_event_samples(event_name)
if samples_results is None:
print "WARNING: Skipping %s" %(event_name)
# Skip files that could not be parsed
continue
# If we're not given a mapping to compressed IDs, check
# that the event IDs do not look compressed
if misc_utils.is_compressed_name(event_name) and \
(use_compressed is None):
print "WARNING: %s looks like a compressed id, but no mapping file " \
"from compressed IDs to event IDs was given! Try: --use-compressed" \
%(event_name)
# Load header/parameters information
samples = samples_results[0]
header = samples_results[1]
header = header[0]
params = parse_sampler_params_from_header(header)
# Get counts information from header
counts_info = samples_results[5]
shape_len = len(shape(samples))
if shape_len < 2:
print "WARNING: Skipping %s -- mishaped file" %(samples_filename)
continue
num_samples, num_isoforms = shape(samples)
output_fields = format_credible_intervals(event_name, samples)
# Add isoforms information to output fields
isoforms_field = get_isoforms_from_header(header)
output_fields.append(isoforms_field)
# Add counts information to output fields
output_fields.append(counts_info['counts'])
output_fields.append(counts_info['assigned_counts'])
gene_info = get_gene_info_from_params(params)
output_fields.append(gene_info["chrom"])
output_fields.append(gene_info["strand"])
output_fields.append(gene_info["mRNA_starts"])
output_fields.append(gene_info["mRNA_ends"])
output_line = "%s\n" %("\t".join(output_fields))
summary_file.write(output_line)
num_events += 1
print " - Summarized a total of %d events." %(num_events)
summary_file.close()
def summarize_sampler_results(samples_dir,
summary_filename,
use_compressed=None):
"""
Given a set of samples from MISO, output a summary file.
"""
summary_file = open(summary_filename, 'w')
header_fields = [
"event_name",
"miso_posterior_mean",
"ci_low",
"ci_high",
"isoforms",
"counts",
"assigned_counts",
# Fields related to gene/event
"chrom",
"strand",
"mRNA_starts",
"mRNA_ends"
]
summary_header = "%s\n" % ("\t".join(header_fields))
summary_file.write(summary_header)
print "Loading events from: %s" % (samples_dir)
print "Writing summary to: %s" % (summary_filename)
all_filenames = get_samples_dir_filenames(samples_dir)
num_events = 0
compressed_ids_to_genes = {}
if use_compressed is not None:
print " - Loading compressed IDs mapping from: %s" % (use_compressed)
# Load mapping from gene IDs to their hashes
compressed_ids_to_genes = misc_utils.load_compressed_ids_to_genes(
use_compressed)
for samples_filename in all_filenames:
# Parse sampler parameters
params = parse_sampler_params(samples_filename)
event_name = get_event_name(samples_filename)
if event_name == None:
print "Skipping %s" % (samples_filename)
continue
# If using compressed event IDs, convert event
# to its real event ID
if use_compressed is not None:
if event_name not in compressed_ids_to_genes:
print "Error: Compressed id %s does not map to any event name." \
%(event_name)
sys.exit(1)
event_name = compressed_ids_to_genes[event_name]
else:
# If we're not given a mapping to compressed IDs, check
# that the event IDs do not look compressed
if misc_utils.is_compressed_name(event_name):
print "WARNING: %s looks like a compressed id, but no mapping file " \
"from compressed IDs to event IDs was given! Try: --use-compressed" \
%(event_name)
# Load samples and header information
samples_results = load_samples(samples_filename)
if samples_results is None:
print "Skipping %s" % (samples_filename)
# Skip files that could not be parsed
continue
samples = samples_results[0]
header = samples_results[1]
header = header[0]
# Get counts information from header
counts_info = samples_results[5]
shape_len = len(shape(samples))
if shape_len < 2:
print "Skipping %s" % (samples_filename)
continue
num_samples, num_isoforms = shape(samples)
output_fields = format_credible_intervals(event_name, samples)
# Add isoforms information to output fields
isoforms_field = get_isoforms_from_header(header)
output_fields.append(isoforms_field)
# Add counts information to output fields
output_fields.append(counts_info['counts'])
output_fields.append(counts_info['assigned_counts'])
gene_info = get_gene_info_from_params(params)
output_fields.append(gene_info["chrom"])
output_fields.append(gene_info["strand"])
output_fields.append(gene_info["mRNA_starts"])
output_fields.append(gene_info["mRNA_ends"])
output_line = "%s\n" % ("\t".join(output_fields))
summary_file.write(output_line)
num_events += 1
print " - Summarized a total of %d events." % (num_events)
summary_file.close()
