Preserving names when extracting genes from gtf.

The resulting BedTool is now in bed format.

libhts/__init__.py

@@ -2,7 +2,7 @@ from subprocess import check_output
 
 __copyright__ = "Copyright (C) 2020-2021 Blaise Li"
 __licence__ = "GNU GPLv3"
-__version__ = 0.5
+__version__ = 0.6
 
 BEDTOOLS_VERSION = check_output(
     ["bedtools", "--version"]).decode("utf-8").strip().split()[-1]

libhts/libhts.py

@@ -46,6 +46,7 @@ import seaborn as sns
 # from rpy2.robjects.packages import importr
 # deseq2 = importr("DESeq2")
 from pybedtools import BedTool
+from pybedtools.featurefuncs import gff2bed
 import pyBigWig
 import networkx as nx
 from libworkflows import texscape
@@ -225,8 +226,15 @@ def id_list_gtf2bed(
 
         def feature_filter(feature):
             return feature[2] == feature_type and feature[id_kwd] in ids
+
+        # def add_name(feature):
+        #     feature.name = feature[id_kwd]
+        #     return feature
+
         gtf = BedTool(gtf_filename)
-        return gtf.filter(feature_filter)
+        # Apparently ignored when later using merge
+        # return gtf.filter(feature_filter).each(add_name)
+        return gtf.filter(feature_filter).each(gff2bed, id_kwd)
 
     # https://stackoverflow.com/a/13243870/1878788
     def empty_bed_generator():