burst reader

Former-commit-id: 60dfc0a8566f703e348ed76609e867ae5af52c3a

Author: bbengfort

Diff for: apps/read_burst.py

@@ -0,0 +1,36 @@
+"""
+Spark application that reads a CloudBurst sequence file and converts it
+into text for review and analysis.
+"""
+
+##########################################################################
+## Imports
+##########################################################################
+
+import sys
+
+from brisera.records import record_from_bytes
+from pyspark import SparkConf, SparkContext
+
+PROG_NAME = "read_burst.py"
+APP_NAME  = "CloudBurst Reader"
+
+if __name__ == "__main__":
+
+    if len(sys.argv) != 3:
+        sys.stderr.write("Usage: %s sequences.br output\n" % PROG_NAME)
+        sys.exit(-1)
+
+    conf = SparkConf().setAppName(APP_NAME)
+    sc   = SparkContext(conf=conf)
+
+    infile  = sys.argv[1]
+    outpath = sys.argv[2]
+
+    print "Converting Sequence File %s to Text using directory %s" % (infile, outpath)
+
+    sequences = sc.sequenceFile(infile)
+    sequences = sequences.map(lambda (k,v): (k, record_from_bytes(v)))
+    sequences.saveAsTextFile(outpath)
+
+