def test_splice_site_str_to_tuple():
from outrigger.validate.check_splice_sites import splice_site_str_to_tuple
test = splice_site_str_to_tuple('GT/AG,AT/AC')
true = 'GT/AG', 'AT/AC'
assert test == true
def execute(self):
valid_splice_sites = check_splice_sites.splice_site_str_to_tuple(
self.valid_splice_sites)
for splice_name, splice_abbrev in common.SPLICE_TYPES:
splice_name_spaces = splice_name.replace('_', ' ').title()
util.progress('Finding valid splice sites in {} ({}) '
'splice type ...'.format(splice_name_spaces,
splice_abbrev.upper()))
isoform_exons = common.SPLICE_TYPE_ISOFORM_EXONS[splice_abbrev]
validated_folder = os.path.join(self.index_folder, splice_abbrev,
'validated')
self.maybe_make_folder(validated_folder)
splice_sites_seriess = []
for isoform, exons in isoform_exons.items():
valid_str = ' or '.join(valid_splice_sites)
util.progress('\tFinding valid splice sites for {isoform} of'
' {splice_name} events which match '
'{valid_splice_sites}'
'...'.format(isoform=isoform,
splice_name=splice_name_spaces,
valid_splice_sites=valid_str))
exon_pairs = zip(exons, exons[1:])
for exonA, exonB in exon_pairs:
util.progress('\t\tFinding splice sites for {exonA} and '
'{exonB} ...'.format(exonA=exonA,
exonB=exonB))
intron_splice_site = self.exon_pair_splice_sites(
exonA, exonB, splice_abbrev)
splice_sites_seriess.append(intron_splice_site)
util.done(4)
util.done(3)
splice_sites = pd.concat(splice_sites_seriess, axis=1)
csv = os.path.join(self.index_folder, splice_abbrev,
'splice_sites.csv')
util.progress('\tWriting splice sites to {csv} ...'.format(
csv=csv))
splice_sites.to_csv(csv)
util.done(3)
n_total = len(splice_sites.groupby(level=0, axis=0))
splice_sites_is_valid = splice_sites.isin(valid_splice_sites)
valid_events_rows = splice_sites_is_valid.all(axis=1)
splice_sites_validated = splice_sites.loc[valid_events_rows]
n_valid = len(splice_sites_validated.groupby(level=0, axis=0))
util.progress("\tValidated {valid}/{total} {splice_name} "
"({splice_abbrev}) events. "
"".format(valid=n_valid, total=n_total,
splice_name=splice_name_spaces,
splice_abbrev=splice_abbrev.upper()))
original_events_csv = os.path.join(self.input_index,
splice_abbrev, EVENTS_CSV)
validated_events_csv = os.path.join(validated_folder, EVENTS_CSV)
util.progress('\tWriting validated events to {csv} ...'.format(
csv=validated_events_csv))
with open(validated_events_csv, 'w') as f_validated:
with open(original_events_csv) as f_original:
for i, line in enumerate(f_original):
if i == 0:
f_validated.write(line)
continue
if line.split(',')[0] in splice_sites_validated.index:
f_validated.write(line)
util.done(3)
