diff qualimap_multi_bamqc.py @ 6:8dff744880cd draft

planemo upload for repository https://github.com/zipho/qualimap2 commit c721c32bc9c559c94c2f8cb9c77aa0c60a9fceb6

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_multi_bamqc.py	Tue Apr 05 04:45:41 2016 -0400
@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError
+import shlex
+import sys
+import logging
+
+log = logging.getLogger(__name__)
+
+
+def qualimap_multi_bamqc(input_file, out_dir, jv_mem_size):
+    #multi-bamqc -r -d ./bamlistinput.txt -outdir ./Kaust_kxdr/variants/qualimap -outformat PDF --java-mem-size=16G
+    cmdline_str = "qualimap multi-bamqc -r -d {} -outdir {} -outformat PDF --java-mem-size={}".format(input_file,
+                                                                                                      out_dir,
+                                                                                                      jv_mem_size)
+    cmdline = new_split(cmdline_str)
+    try:
+        check_call(cmdline)
+    except CalledProcessError:
+        print("Error running the qualimap multi bamqc", file=sys.stderr)
+
+
+def new_split(value):
+    lex = shlex.shlex(value)
+    lex.quotes = '"'
+    lex.whitespace_split = True
+    lex.commenters = ''
+    return list(lex)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate Bam Quality Statistics")
+    parser.add_argument('--input_file')
+    parser.add_argument('--out_dir', default="/tmp/bamstats")
+    parser.add_argument('--java_mem_size', default="8G")
+
+    args = parser.parse_args()
+
+    qualimap_multi_bamqc(args.input_file, args.out_dir, args.java_mem_size)
+
+
+if __name__ == "__main__": main()
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