Merge pull request #82 from JiguangPeng/master

[#75] ReadExtractor support absolute path
iprada · Jul 2, 2022 · e1d122a · e1d122a
2 parents ed88ff6 + f396528
commit e1d122a
Showing 1 changed file with 9 additions and 3 deletions.
diff --git a/circlemap/extract_circle_SV_reads.py b/circlemap/extract_circle_SV_reads.py
@@ -61,7 +61,10 @@ def extract_sv_circleReads(self):
         os.chdir(self.working_dir)
 
         #input
-        raw_bam = ps.AlignmentFile(self.working_dir + "/" + self.sorted_bam, "rb")
+        if os.path.isabs(self.sorted_bam):
+            raw_bam = ps.AlignmentFile(self.sorted_bam, "rb")
+        else:
+            raw_bam = ps.AlignmentFile(self.working_dir + "/" + self.sorted_bam, "rb")
 
         #HD the tag for the header line. SO indicates sorting order of the alignements
         if 'HD' in raw_bam.header:
@@ -85,7 +88,10 @@ def extract_sv_circleReads(self):
 
 
 
-        circle_sv_reads = ps.AlignmentFile(self.working_dir + "/" + self.output_bam , "wb", template=raw_bam)
+        if os.path.isabs(self.output_bam):
+            circle_sv_reads = ps.AlignmentFile(self.output_bam , "wb", template=raw_bam)
+        else:
+            circle_sv_reads = ps.AlignmentFile(self.working_dir + "/" + self.output_bam , "wb", template=raw_bam)
 
 
         #modify the tag to unsorted
@@ -222,4 +228,4 @@ def extract_sv_circleReads(self):
 
             print("finished extracting reads. Elapsed time:", (end - begin) / 60, "mins")
 
-            print("Thanks for using Circle-Map")
+            print("Thanks for using Circle-Map")