From df144d1b335c82dcc02252a0274e150363b69165 Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Tue, 5 Nov 2024 13:31:53 -0500 Subject: [PATCH] use explicit namespace in docstrings of long_range_interaction --- pybedtools/contrib/long_range_interaction.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pybedtools/contrib/long_range_interaction.py b/pybedtools/contrib/long_range_interaction.py index 8baffe74..a3555a5c 100644 --- a/pybedtools/contrib/long_range_interaction.py +++ b/pybedtools/contrib/long_range_interaction.py @@ -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) @@ -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)) @@ -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