def build_tree_from_group(group, ref_dataframe, coord_func, bar=None):
'''
Build an IntervalTree from a sub-DataFrame, for groupby() operations
'''
tree = IntervalTree()
for idx, row in group.iterrows():
if bar is not None:
bar.update()
start, end, chrom, strand = coord_func(row)
tree.insert_interval(DataFrameInterval(idx, ref_dataframe, start, end,
chrom=chrom, strand=strand))
return tree
def build_forest_from_groups(grouped_df, reference_df, coord_func, bar=None):
forest = IntervalForest()
for key, group in grouped_df:
tree = IntervalTree()
for idx, row in group.iterrows():
start, end, chrom, strand = coord_func(row)
tree.insert_interval(DataFrameInterval(idx, reference_df, start, end,
chrom=chrom, strand=strand))
if bar is not None:
bar.update()
forest.add_tree(key, tree)
return forest
def build_tree_from_group(group, ref_dataframe, coord_func, bar=None):
'''
Build an IntervalTree from a sub-DataFrame, for groupby() operations
'''
tree = IntervalTree()
for idx, row in group.iterrows():
if bar is not None:
bar.update()
start, end, chrom, strand = coord_func(row)
tree.insert_interval(
DataFrameInterval(idx,
ref_dataframe,
start,
end,
chrom=chrom,
strand=strand))
return tree
def build_forest_from_groups(grouped_df, reference_df, coord_func, bar=None):
forest = IntervalForest()
for key, group in grouped_df:
tree = IntervalTree()
for idx, row in group.iterrows():
start, end, chrom, strand = coord_func(row)
tree.insert_interval(
DataFrameInterval(idx,
reference_df,
start,
end,
chrom=chrom,
strand=strand))
if bar is not None:
bar.update()
forest.add_tree(key, tree)
return forest
