def test_calculate_psi(event_annotation, reads2d, isoform1_junctions,
isoform2_junctions, psi_df, summary_df):
from outrigger.psi.compute import calculate_psi
true_psi = psi_df
true_summary = summary_df
test_psi, test_summary = calculate_psi(event_annotation, reads2d,
isoform1_junctions,
isoform2_junctions)
# When psi is written to CSV, only the index name is preserved, not the
# column names so need to get rid of it for these comparisons
test_psi.columns.name = None
pdt.assert_frame_equal(test_psi, true_psi)
pdt.assert_frame_equal(test_summary, true_summary)
def test_calculate_psi(event_annotation, reads2d,
isoform1_junctions, isoform2_junctions,
psi_df, summary_df):
from outrigger.psi.compute import calculate_psi
true_psi = psi_df
true_summary = summary_df
test_psi, test_summary = calculate_psi(event_annotation, reads2d,
isoform1_junctions,
isoform2_junctions)
# When psi is written to CSV, only the index name is preserved, not the
# column names so need to get rid of it for these comparisons
test_psi.columns.name = None
pdt.assert_frame_equal(test_psi, true_psi)
pdt.assert_frame_equal(test_summary, true_summary)
def execute(self):
"""Calculate percent spliced in (psi) of splicing events"""
logger = logging.getLogger('outrigger.psi')
if self.debug:
logger.setLevel(10)
junction_reads = self.csv()
metadata_csv = os.path.join(self.junctions_folder, METADATA_CSV)
self.junction_metadata(junction_reads, metadata_csv)
junction_reads_2d = junction_reads.pivot(index=self.sample_id_col,
columns=self.junction_id_col,
values=self.reads_col)
junction_reads_2d.fillna(0, inplace=True)
junction_reads_2d = junction_reads_2d.astype(int)
logger.debug('\n--- Splice Junction reads ---')
logger.debug(repr(junction_reads.head()))
psis = []
for splice_name, splice_abbrev in outrigger.common.SPLICE_TYPES:
filename = self.maybe_get_validated_events(splice_abbrev)
if not os.path.exists(filename):
util.progress('No {name} ({abbrev}) events found, '
'skipping.'. format(name=splice_name,
abbrev=splice_abbrev))
continue
# event_type = os.path.basename(filename).split('.csv')[0]
util.progress('Reading {name} ({abbrev}) events from {filename}'
' ...'.format(name=splice_name, abbrev=splice_abbrev,
filename=filename))
event_annotation = pd.read_csv(filename, index_col=0,
low_memory=self.low_memory)
util.done()
isoform_junctions = outrigger.common.ISOFORM_JUNCTIONS[
splice_abbrev]
logger.debug('\n--- Splicing event annotation ---')
logger.debug(repr(event_annotation.head()))
util.progress(
'Calculating percent spliced-in (Psi) scores on '
'{name} ({abbrev}) events ...'.format(
name=splice_name, abbrev=splice_abbrev))
# Splice type percent spliced-in (psi) and summary
type_psi, summary = compute.calculate_psi(
event_annotation, junction_reads_2d,
min_reads=self.min_reads, n_jobs=self.n_jobs,
method=self.method,
uneven_coverage_multiplier=self.uneven_coverage_multiplier,
**isoform_junctions)
# Write this event's percent spliced-in matrix
csv = os.path.join(self.psi_folder, splice_abbrev,
'psi.csv'.format(splice_abbrev))
util.progress('Writing {name} ({abbrev}) Psi values to {filename}'
' ...'.format(name=splice_name, abbrev=splice_abbrev,
filename=csv))
self.maybe_make_folder(os.path.dirname(csv))
type_psi.to_csv(csv, na_rep='NA')
# Write this event's summary of events and why they weren't or were
# calculated Psi on
csv = os.path.join(self.psi_folder, splice_abbrev,
'summary.csv'.format(splice_abbrev))
util.progress('Writing {name} ({abbrev}) event summaries (e.g. '
'number of reads, why an event does not have a Psi '
'score) to {filename} ...'
''.format(name=splice_name, abbrev=splice_abbrev,
filename=csv))
self.maybe_make_folder(os.path.dirname(csv))
summary.to_csv(csv, na_rep='NA', index=False)
psis.append(type_psi)
util.done()
util.progress('Concatenating all calculated psi scores '
'into one big matrix...')
splicing = pd.concat(psis, axis=1)
util.done()
splicing = splicing.T
csv = os.path.join(self.psi_folder, 'outrigger_psi.csv')
util.progress('Writing a samples x features matrix of Psi '
'scores to {} ...'.format(csv))
splicing.to_csv(csv, na_rep='NA')
util.done()
