--- a/bismark_deduplicate_wrapper.py	Fri Oct 04 11:33:27 2019 -0400
+++ b/bismark_deduplicate_wrapper.py	Thu Apr 22 17:05:46 2021 +0000
@@ -4,11 +4,10 @@
 import logging
 import os
 import shutil
+import signal
 import subprocess
 import sys
-import signal
 import tempfile
-from glob import glob
 
 
 def stop_err(logger, msg):
@@ -24,17 +23,21 @@
 
 
 def log_subprocess_output(logger, pipe):
-    for line in iter(pipe.readline, b''):
+    for line in iter(pipe.readline, b""):
         logger.debug(line.decode().rstrip())
 
 
 def get_arg():
     parser = argparse.ArgumentParser()
-    parser.add_argument('--single_or_paired',  dest='single_or_paired')
-    parser.add_argument('--input', dest='input', metavar='input')
-    parser.add_argument('--output_report', dest='output_report', metavar='output_report')
-    parser.add_argument('--output_bam', dest='output_bam', metavar='output_report')
-    parser.add_argument('--log_report', dest='log_report', metavar='log_filename', type=str)
+    parser.add_argument("--single_or_paired", dest="single_or_paired")
+    parser.add_argument("--input", dest="input", metavar="input")
+    parser.add_argument(
+        "--output_report", dest="output_report", metavar="output_report"
+    )
+    parser.add_argument("--output_bam", dest="output_bam", metavar="output_report")
+    parser.add_argument(
+        "--log_report", dest="log_report", metavar="log_filename", type=str
+    )
     args = parser.parse_args()
     return args
 
@@ -42,7 +45,7 @@
 def __main__():
     args = get_arg()
 
-    logger = logging.getLogger('bismark_deduplicate_wrapper')
+    logger = logging.getLogger("bismark_deduplicate_wrapper")
     logger.setLevel(logging.DEBUG)
     ch = logging.StreamHandler(sys.stdout)
     if args.log_report:
@@ -55,27 +58,39 @@
     logger.addHandler(ch)
 
     # ensure the input has a .bam suffix
-    tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
+    tmp_dir = tempfile.mkdtemp(prefix="tmp", suffix="")
     os.chdir(tmp_dir)
-    default_reads_name = 'submitted_reads.bam'
+    default_reads_name = "submitted_reads.bam"
     os.symlink(args.input, default_reads_name)
 
-    single_or_paired = '-s' if args.single_or_paired == 'single' else '-p'
-    cmd = ['deduplicate_bismark', single_or_paired, default_reads_name, '--bam']
+    single_or_paired = "-s" if args.single_or_paired == "single" else "-p"
+    cmd = ["deduplicate_bismark", single_or_paired, default_reads_name, "--bam"]
     logger.info("Deduplicating with: '%s'", " ".join(cmd))
-    process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
-                               preexec_fn=restore_sigpipe)
+    process = subprocess.Popen(
+        cmd,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+        preexec_fn=restore_sigpipe,
+    )
     proc_out, proc_err = process.communicate()
     logger.info(proc_out)
     if process.returncode != 0:
-        stop_err(logger, "Bismark deduplication error (also check the log file if any)!\n%s" % proc_err)
+        stop_err(
+            logger,
+            "Bismark deduplication error (also check the log file if any)!\n%s"
+            % proc_err,
+        )
 
-    deduplicated_out_name = 'submitted_reads.deduplicated.bam'
-    deduplicated_report_name = 'submitted_reads.deduplication_report.txt'
+    deduplicated_out_name = "submitted_reads.deduplicated.bam"
+    deduplicated_report_name = "submitted_reads.deduplication_report.txt"
     logger.debug("Moving '%s' to galaxy: '%s'.", deduplicated_out_name, args.output_bam)
-    shutil.move(deduplicated_out_name, args.output_bam )
-    logger.debug("Moving '%s' to galaxy: '%s'.", deduplicated_report_name, args.output_report)
-    shutil.move('submitted_reads.deduplication_report.txt', args.output_report)
+    shutil.move(deduplicated_out_name, args.output_bam)
+    logger.debug(
+        "Moving '%s' to galaxy: '%s'.", deduplicated_report_name, args.output_report
+    )
+    shutil.move("submitted_reads.deduplication_report.txt", args.output_report)
     logger.debug("Done.")
 
-if __name__=="__main__": __main__()
\ No newline at end of file
+
+if __name__ == "__main__":
+    __main__()