def expand_row(row):
"""Parse a BED row.
Args:
List[str]: BED row
Returns:
dict: formatted BED row as a dict
Raises:
BedFormattingError: failure to parse first three columns
"""
try:
data = {
'chrom': row[0],
'chromStart': int(row[1]),
'chromEnd': int(row[2])
}
except IndexError:
raise BedFormattingError('make sure fields are tab-separated')
except ValueError:
raise BedFormattingError("positions malformatted: {}".format(row))
try:
data['score'] = int(list_get(row, 4))
except ValueError:
raise BedFormattingError('invalid BED syntax, score column is int')
data['name'] = list_get(row, 3)
data['strand'] = list_get(row, 5)
element_combos = extra_fields(row[6:8])
data['elements'] = element_combos
data['extra_fields'] = row[8:]
return data
def expand_row(row):
"""Parse a BED row.
Args:
List[str]: BED row
Returns:
dict: formatted BED row as a dict
Raises:
BedFormattingError: failure to parse first three columns
"""
try:
data = {"chrom": row[0], "chromStart": int(row[1]), "chromEnd": int(row[2])}
except IndexError:
raise BedFormattingError("make sure fields are tab-separated")
except ValueError:
raise BedFormattingError("positions malformatted: {}".format(row))
try:
data["score"] = int(list_get(row, 4))
except ValueError:
raise BedFormattingError("invalid BED syntax, score column is int")
data["name"] = list_get(row, 3)
data["strand"] = list_get(row, 5)
element_combos = extra_fields(row[6:8])
data["elements"] = element_combos
data["extra_fields"] = row[8:]
return data
def completeness_levels(self):
"""Return a list of included completeness levels."""
metrics = (self.query(ExonStatistic.metric).distinct(
ExonStatistic.metric))
# for all completeness levels, extract the level as int and full name
levels = ((int(field[0].split('_')[-1]), field[0]) for field in metrics
if field[0].startswith('completeness'))
# sort them based on the level int
sorted_levels = sorted(levels, key=lambda level: list_get(level, 0))
return sorted_levels
def completeness_levels(self):
"""Return a list of included completeness levels."""
metrics = (self.query(ExonStatistic.metric)
.distinct(ExonStatistic.metric))
# for all completeness levels, extract the level as int and full name
levels = ((int(field[0].split('_')[-1]), field[0])
for field in metrics
if field[0].startswith('completeness'))
# sort them based on the level int
sorted_levels = sorted(levels, key=lambda level: list_get(level, 0))
return sorted_levels