BAM file processing according to AnnoJ data type.

nextgen/AnnoJBAM.py

@@ -0,0 +1,42 @@
+#!/usr/bin/python 
+"""
+Write a BAM file content to a plain text format. 
+Usage: python bam_to_txt.py in.bam > out.txt  
+"""
+import re, sys 
+import pysam 
+
+def AnnoJ_BAM(bam_read):
+    for rec in sam_reader.fetch():
+        orient=None
+        for atb in rec.tags:
+            if atb[0]=='XS':
+                orient=atb[1]
+        print rec.qname, orient, rec.pos, rec.qlen, sam_reader.getrname(rec.rname), rec.query
+
+def sort_BAM_TAGS(bam_read):
+    """
+    """
+    for line in sys.stdin:
+        print line.strip('\n\r')
+    outsam=pysam.Samfile("-", "w", template = bam_read)
+    for rec in bam_read.fetch():
+        new_cont=rec.tags
+        new_cont.insert(0, rec.tags[-1])
+        new_cont.pop()
+        rec.tags=new_cont
+        outsam.write(rec)
+    outsam.close()
+
+def __main__():
+
+    try:
+        bam_file=sys.argv[1]
+    except:
+        print __doc__
+        sys.exit(1)
+    sam_reader = pysam.Samfile(bam_file, "rb")
+    sort_BAM_TAGS(sam_reader)
+    sam_reader.close()
+
+if __name__=="__main__":__main__()