Validating walker for lots of bam files

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@10 348d0f76-0448-11de-a6fe-93d51630548a

python/SpawnValidationJobs.py

@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+
+import getopt, sys, os, string
+from farm_commands import *
+
+def picardCMD(name, **keywords ):
+    cmd = name
+    for key, value in keywords.iteritems():
+        cmd += ' ' + key + "=" + str(value)
+    return cmd
+
+def spawnValidationJob( input_file, output_head, farm, maxErrors):
+    validate_exe = "ValidateSAM"
+    output_file = output_head + '.stdout'
+
+    if regenExistingFiles or not os.path.exists(output_file):
+        cmd_str = picardCMD( validate_exe, I=input_file, M=maxErrors )
+        if farm == "":
+             cmd_str += " > " + output_file
+        cmd(cmd_str, farm, output_head, just_print_commands=justPrintCommands)
+    
+def usage():
+    print "Required arguments:"
+    print "  -d         Directory to grab all sam/bam files from"
+    print
+    print "Optional arguments:"
+    print "  -f QUEUE   Farm jobs to QUEUE on LSF"
+    print
+    print "  -m MAXERRORS  Maximum number of errors to detect before aborting"
+    print
+
+
+def get_all_sam_files(dir):
+    files = []
+    
+    for dirpath, dirnames, filenames in os.walk(dir):
+        for filename in filenames:
+            base, ext = os.path.splitext(filename)
+            if ext.lower() in ['.sam', '.bam']:
+                files.append( os.path.join( dirpath, filename ) )
+            #print filename, base, ext
+
+    return files
+
+def output_filename( input_file ):
+    parts = filter(lambda x: x.strip() <> '', input_file.split("/"))
+    print parts
+    return ".".join(parts) + ".validation" 
+
+justPrintCommands = False
+regenExistingFiles = False
+
+if __name__ == "__main__":
+    opts = None
+    try:
+        opts, args = getopt.getopt(sys.argv[1:], "d:f:m:r", ["dir","farm","maxErrors", "regenExistingFiles"])
+    except getopt.GetoptError:
+        print sys.argv
+        usage()
+        sys.exit(2)
+
+    dir = ""
+    mapper_str = "all"
+    farm_sub = False
+    maxErrors = 1000
+
+    for opt, arg in opts:
+        print opt, arg
+        if opt in ("-d", "--dir"):
+            dir = arg
+        if opt in ("-f", "--farm"):
+            farm_sub = arg
+        if opt in ("-m", "--maxErrors"):
+            maxErrors = arg
+        if opt in ("-r", "--regenExistingFiles"):
+            regenExistingFiles = True            
+    if dir == "":
+        usage()
+        sys.exit(2)
+
+    input_files = get_all_sam_files(dir)
+    print 'Processing files: N=', len(input_files)
+    for input_file in input_files:
+        print '  ->', input_file
+        
+    for input_file in input_files:
+        output_file = output_filename( input_file )
+        print input_file, "=>", output_file
+        spawnValidationJob( input_file, output_file, farm_sub, maxErrors )
+        
+        
+