diff qualimap_bamqc.py @ 0:d87d6c0c27f5 draft

planemo upload for repository https://github.com/zipho/qualimap2 commit fb67f375d3ae592c62f73d647d8afa19b79037c0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qualimap_bamqc.py	Wed Mar 30 03:19:15 2016 -0400
@@ -0,0 +1,42 @@
+#!/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_bamqc( bam_filename, genomecov_file, out_dir, pdf_file, jv_mem_size):
+    #qualimap bamqc -bam R.bam.sorted_dedup.bam_realigned.bam -oc ./test.genomecov  -outdir ./Kaust_kxdr/variants/qualimap/bamqc_report --outfile test.pdf --java-mem-size=16G
+    cmdline_str = "qualimap bamqc -bam {} -oc {} -outdir {} --outfile {} --java-mem-size={}".format( bam_filename,
+                                                                                                     genomecov_file,
+                                                                                                     out_dir,
+                                                                                                     pdf_file,
+                                                                                                     jv_mem_size)
+    cmdline = newSplit(cmdline_str)
+    try:
+        check_call(cmdline)
+    except CalledProcessError:
+        print("Error running the qualimap bamqc", file=sys.stderr)
+
+def newSplit(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_genome_file', default="bam_stats.genomecov")
+    parser.add_argument('--out_dir',  default="/tmp/bamstats")
+    parser.add_argument('--out_pdf_file', default="bam_stats.pdf")
+    parser.add_argument('--java_mem_size', default="8G" )
+
+    args = parser.parse_args()
+   
+    qualimap_bamqc(args.input_file, args.out_genome_file, args.out_dir, args.out_pdf_file, args.java_mem_size)
+
+if __name__ == "__main__": main()