0.1.6, fix issue for unsorted bed in bedtools merge

Runsheng · Jan 24, 2023 · 6025fa3 · 6025fa3
1 parent a019314
commit 6025fa3
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Showing 3 changed files with 4 additions and 4 deletions.
diff --git a/test/flow_test.py b/test/flow_test.py
@@ -117,7 +117,7 @@ def test_prepare_run_gene_novel(self):
         :return:
         """
         # parameters
-        wkdir="/t1/shoudong_488/test/tracktest"
+        wkdir="/t1/shoudong_488/test/trackall"
         prefix="488_aba_1"
         gff_bed="../gene.bed_s"
         nano_bed="../488_aba_1_s.bed"

diff --git a/trackcluster/__init__.py b/trackcluster/__init__.py
@@ -1,5 +1,5 @@
 # For relative imports to work in Python 3.6
 import os, sys
 sys.path.append(os.path.dirname(os.path.realpath(__file__)))
-__version__="0.1.5"
+__version__="0.1.6"
 __all__ = []
diff --git a/trackcluster/pre.py b/trackcluster/pre.py
@@ -63,10 +63,10 @@ def wrapper_bedtools_merge(bigg_file, out):
     # merge with strandness, report to col5
     # bedtools 2.26, can use -s -c 4 -o count
     # bedtools 2.30, must use -s c 6 -o distinct,count
-    cmd="bedtools merge -nonamecheck -s  -c 6 -o distinct,count -i {biggfile} > {out}".format(
+    cmd="bedtools sort -i {biggfile} > {biggfile}_s && bedtools merge -nonamecheck -s  -c 6 -o distinct,count -i {biggfile}_s > {out}".format(
         biggfile=bigg_file, out=out
     )
-    _=myexe(cmd)
+    myexe(cmd)
 
     return out