From 1843ade546071552aa5fff11eabfabbadfb43d29 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 16 Jul 2019 18:25:14 +0200
Subject: [PATCH] Fix empty BedTool: need to pass file name, not fh.
---
libhts/libhts.py | 25 ++++++++++++-------------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/libhts/libhts.py b/libhts/libhts.py
index 6631039..b4bfc47 100644
--- a/libhts/libhts.py
+++ b/libhts/libhts.py
@@ -189,19 +189,18 @@ def id_list_gtf2bed(identifiers, gtf_filename, feature_type="transcript", id_kwd
in the feature annotations in the gtf_file. These feature IDs will be
matched against the elements in *identifiers*.
"""
- with open(gtf_filename, "r") as gtf_file:
- gtf = BedTool(gtf_file)
- if identifiers:
- ids = set(identifiers)
- def feature_filter(feature):
- return feature[2] == feature_type and feature[id_kwd] in ids
- return gtf.filter(feature_filter)
- else:
- # https://stackoverflow.com/a/13243870/1878788
- def empty_bed_generator():
- return
- yield
- return empty_bed_generator()
+ if identifiers:
+ ids = set(identifiers)
+ def feature_filter(feature):
+ return feature[2] == feature_type and feature[id_kwd] in ids
+ gtf = BedTool(gtf_filename)
+ return gtf.filter(feature_filter)
+ else:
+ # https://stackoverflow.com/a/13243870/1878788
+ def empty_bed_generator():
+ return
+ yield
+ return empty_bed_generator()
def make_empty_bigwig(filename, chrom_sizes):
--
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