def _subtraction(scdf, ocdf, **kwargs):
if ocdf.empty or scdf.empty:
return scdf
strandedness = kwargs["strandedness"]
strand = True if strandedness else False
chromosome = scdf.Chromosome.head(1).iloc[0]
kwargs["chromosome"] = chromosome
if "Strand" in ocdf and strand:
strand = scdf.Strand.head(1).iloc[0]
kwargs["strand"] = strand
o = NCLS(ocdf.Start.values, ocdf.End.values, ocdf.index.values)
idx_self, new_starts, new_ends = o.set_difference_helper(
scdf.Start.values, scdf.End.values, scdf.index.values,
scdf.__num__.values)
missing_idx = pd.Index(scdf.index).difference(idx_self)
idx_to_drop = new_starts != -1
new_starts = new_starts[idx_to_drop]
new_ends = new_ends[idx_to_drop]
idx_self = idx_self[idx_to_drop]
new_starts = pd.Series(new_starts, index=idx_self)
new_ends = pd.Series(new_ends, index=idx_self)
scdf = scdf.reindex(missing_idx.union(idx_self)).sort_index()
new_starts = new_starts.sort_index()
new_ends = new_ends.sort_index()
if len(idx_self):
scdf.loc[scdf.index.isin(idx_self), "Start"] = new_starts.values
scdf.loc[scdf.index.isin(idx_self), "End"] = new_ends.values
if not scdf.empty:
return scdf
else:
return None
def _subtraction(scdf, ocdf, **kwargs):
chromosome, strand = parse_grpby_key(kwargs["key"])
if ocdf.empty or scdf.empty:
return scdf
strandedness = kwargs["strandedness"]
strand = True if strandedness else False
oc = _cluster(ocdf, chromosome, strand)
o = NCLS(oc.Start.values, oc.End.values, oc.index.values)
idx_self, new_starts, new_ends = o.set_difference_helper(
scdf.Start.values, scdf.End.values, scdf.index.values)
missing_idx = pd.Index(scdf.index).difference(idx_self)
idx_to_drop = new_starts != -1
new_starts = new_starts[idx_to_drop]
new_ends = new_ends[idx_to_drop]
idx_self = idx_self[idx_to_drop]
new_starts = pd.Series(new_starts, index=idx_self).sort_index()
new_ends = pd.Series(new_ends, index=idx_self).sort_index()
idx_self = np.sort(idx_self)
scdf = scdf.reindex(missing_idx.union(idx_self))
if len(idx_self):
scdf.loc[scdf.index.isin(idx_self), "Start"] = new_starts
scdf.loc[scdf.index.isin(idx_self), "End"] = new_ends
return scdf