Helper utility for merging BAM files

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@345 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:10:41 +00:00 · 2009-04-09 20:10:41 +00:00 · 49b2622e3d
parent 8e2f5471a1
commit 49b2622e3d
1 changed files with 51 additions and 0 deletions
--- a/python/MergeBAMBatch.py
+++ b/python/MergeBAMBatch.py
@ -0,0 +1,51 @@
+import farm_commands
+import os.path
+import sys
+from optparse import OptionParser
+from datetime import date
+import glob
+import operator
+
+MERGE_BIN = '/seq/software/picard/current/bin/MergeSamFiles.jar'
+bam_ext = '.bam'
+
+if __name__ == "__main__":
+    usage = "usage: %prog [options]"
+    parser = OptionParser(usage=usage)
+    parser.add_option("-f", "--farm", dest="farm_sub",
+                        type="string", default=None,
+                        help="Farm queue to send processing jobs to")
+    parser.add_option("-d", "--dir", dest="output_dir",
+                        type="string", default="./",
+                        help="Output directory")
+    parser.add_option("-i", "--ignoreExistingFiles", dest="ignoreExistingFiles",
+                        action='store_true', default=False,
+                        help="Ignores already written files, if present")
+
+    (OPTIONS, args) = parser.parse_args()
+    if len(args) != 1:
+        parser.error("incorrect number of arguments")
+
+    directory = OPTIONS.output_dir
+    today = date.today()
+    time_stamp = today.isoformat()
+    
+    for line in open(args[0]):
+        s = line.split()
+        if ( s <> [] and s[0] <> '#' ):
+            merged_filename = s[0]
+            output = os.path.join(directory, merged_filename + '.stdout')
+            current_link = os.path.join(directory, merged_filename + bam_ext)
+            stamped_filename = os.path.join(directory, merged_filename + '_' + time_stamp + bam_ext)
+            sources = reduce( operator.__add__, map( glob.glob, s[1:] ), [] )
+            
+            if OPTIONS.ignoreExistingFiles or not os.path.exists(stamped_filename):
+                cmd = 'java -Xmx4096m -jar ' + MERGE_BIN + ' O=' + stamped_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources))
+                print cmd
+                farm_commands.cmd(cmd, OPTIONS.farm_sub, output)
+                
+            if OPTIONS.ignoreExistingFiles or not os.path.lexists(current_link):
+                print 'os.path.exists(current_link)', os.path.exists(current_link)
+                cmd = 'ln -s ' + stamped_filename + " " + current_link
+                farm_commands.cmd(cmd, False, '')
+