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use explicit namespace in docstrings of long_range_interaction
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daler committed Nov 5, 2024
1 parent f4a50b1 commit df144d1
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions pybedtools/contrib/long_range_interaction.py
Original file line number Diff line number Diff line change
Expand Up @@ -120,7 +120,7 @@ def tag_bedpe(bedpe, queries, verbose=False):
>>> queries = OrderedDict()
>>> queries['tss'] = tsses
>>> queries['pk'] = peaks
>>> iterator, n, extra = tag_bedpe(bedpe, queries)
>>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, queries)
>>> print(n)
2
>>> print(extra)
Expand Down Expand Up @@ -280,7 +280,7 @@ def cis_trans_interactions(iterator, n, extra, verbose=True):
>>> queries = OrderedDict()
>>> queries['tss'] = tsses
>>> queries['pk'] = peaks
>>> iterator, n, extra = tag_bedpe(bedpe, queries)
>>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, queries)
>>> for (label, group1, group2) in iterator:
... group1 = sorted(group1, key=lambda x: str(x))
... group2 = sorted(group2, key=lambda x: str(x))
Expand All @@ -303,8 +303,8 @@ def cis_trans_interactions(iterator, n, extra, verbose=True):
and that they are also connected to gene3:
>>> import pandas; pandas.set_option('display.max_columns', 10)
>>> iterator, n, extra = tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks})
>>> df = cis_trans_interactions(iterator, n, extra)
>>> iterator, n, extra = pybedtools.contrib.long_range_interaction.tag_bedpe(bedpe, {'tss': tsses, 'pk': peaks})
>>> df = pybedtools.contrib.long_range_interaction.cis_trans_interactions(iterator, n, extra)
>>> print(df.sort_values(list(df.columns)).reset_index(drop=True))
target_label target_name cis_label cis_name distal_label distal_name label
0 pk peak1 tss gene1 . . pair2
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