merged

Author: Florian Finkernagel finkernagel@imt.uni-marburg.de

src/mbf/align/post_process.py

@@ -261,6 +261,7 @@ def process(self, input_bam_name, output_bam_name, result_dir):
     def register_qc(self, new_lane):
         pass  # pragma: no
 
+
 class R2Only(_PostProcessor):
     """Remove all r2 (0x40 reads)
     and turn a paired end alignment into single reads for downstream analyses
@@ -289,7 +290,6 @@ def register_qc(self, new_lane):
         pass  # pragma: no
 
 
-
 class AddChr(_PostProcessor):
     def __init__(self):
         self.name = "AddChr"
@@ -332,6 +332,48 @@ def process(self, input_bam_name, output_bam_name, result_dir):
         out.close()
 
 
+class RemoveChr(_PostProcessor):
+    def __init__(self):
+        self.name = "RemoveChr"
+        self.result_folder_name = self.name
+
+    def register_qc(self, new_lane):
+        pass  # pragma: no
+
+    def process(self, input_bam_name, output_bam_name, result_dir):
+        import pysam
+
+        input = pysam.Samfile(input_bam_name)
+        names_and_lengths = [(k, v) for (k, v) in zip(input.references, input.lengths)]
+
+        header = input.header.to_dict()
+        if "PG" not in header:
+            header["PG"] = []
+        header["PG"].append(
+            {
+                "ID": "mbf_align_remove_chr",
+                "PN": "RemoveChr",
+                "VN": "0.1",
+                "CL": "",
+            }
+        )
+        del header["SQ"]
+        header["SQ"] = []
+        for k, length in names_and_lengths:
+            new_name = k[3:] if k.startswith("chr") else k
+            header["SQ"].append({"LN": length, "SN": new_name})
+
+        out = pysam.Samfile(
+            output_bam_name,
+            "wb",
+            header=header,
+        )
+        for read in input.fetch(until_eof=True):
+            out.write(read)
+        input.close()
+        out.close()
+
+
 class AddChrAndFilter(_PostProcessor):
     def __init__(self, accepted_chrs):
         """accepted_chrs is in terms of the input list, not the chr added list"""
@@ -362,4 +404,3 @@ def get_dependencies(self):
                 "AddChrAndFilter.mbf_bam.version", mbf_bam.__version__
             ),
         ]
-