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From df144d1b335c82dcc02252a0274e150363b69165 Mon Sep 17 00:00:00 2001
From: Ryan Dale <ryan.dale@nih.gov>
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
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