diff bismark_deduplicate/bismark_deduplicate_wrapper.py @ 7:fcadce4d9a06 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bismark_deduplicate/bismark_deduplicate_wrapper.py	Sat May 06 13:18:09 2017 -0400
@@ -0,0 +1,66 @@
+#!/usr/bin/python
+
+import argparse
+import os
+import re
+import shutil
+import subprocess
+import sys
+import tempfile
+import logging
+from glob import glob
+
+def cleanup_before_exit(tmp_dir):
+    if tmp_dir and os.path.exists(tmp_dir):
+        shutil.rmtree(tmp_dir)
+
+def get_arg():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--tool_dir', dest='tool_dir', action='store', nargs=1, metavar='tool_dir', type=str)
+    parser.add_argument('-p', action='store_true')
+    parser.add_argument('-s', action='store_true')
+    parser.add_argument('--input', dest='input', action='store', nargs=1, metavar='input', type=str)
+    parser.add_argument('--output_report', dest='output_report', action='store', nargs=1, metavar='output_report', type=str)
+    parser.add_argument('--output_bam', dest='output_bam', action='store', nargs=1, metavar='output_report', type=str)
+    parser.add_argument('--log_report', dest='log_report', action='store', nargs=1, metavar='log_filename', type=str)
+    args = parser.parse_args()
+    return args
+
+def __main__():
+    args = get_arg()
+
+    tmp_dir = tempfile.mkdtemp(prefix='tmp', suffix='')
+    os.chdir(tmp_dir)
+
+    if args.log_report:
+        logging.basicConfig(level=logging.INFO, filename=args.log_report[0], filemode="a+", format='%(message)s')
+    else:
+        logging.basicConfig(level=logging.INFO, filename=os.path.join(tmp_dir, 'log_report.txt'), filemode="a+", format='%(message)s')
+
+    default_reads_name = 'submitted_reads.bam'
+    os.symlink(args.input[0], default_reads_name)
+
+    if args.p is True:
+        sPaired = '-p'
+    if args.s is True:
+        sPaired = '-s'
+
+    cmd = 'perl %s %s duplicated_reads.bam --bam' % (os.path.join(args.tool_dir[0], 'deduplicate_bismark'), sPaired)
+    logging.info('COMMAND LINE:\n\n%s' % cmd)
+
+    proc = subprocess.Popen(['perl', os.path.join(args.tool_dir[0], 'deduplicate_bismark'), sPaired, default_reads_name, '--bam'], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+    proc_out, proc_err = proc.communicate()
+
+    logging.info("__________________________________________________________________\n")
+    logging.info("BISMARK DEDUPLICATE STDOUT:\n\n%s" % proc_out)
+    if proc_err:
+        logging.critical("__________________________________________________________________\n")
+        logging.critical("BISMARK DEDUPLICATE WARNING:\n\n%s" % proc_err)
+        sys.exit("Dedpulicate Bismark crashed with the folowing error message:\n%s" % proc_err)
+
+    shutil.move( glob('*deduplicated.bam')[0], args.output_bam[0] )
+    shutil.move( glob('*deduplication_report.txt')[0], args.output_report[0])
+
+    cleanup_before_exit(tmp_dir)
+
+if __name__=="__main__": __main__()
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