[Swift-commit] r7239 - in SwiftApps/Swift-MapRed/mapred_combiner_V4: . examples/blast

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2013-10-28 14:09:37 -0500 (Mon, 28 Oct 2013)
New Revision: 7239

Added:
   SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/sequence.seq
Modified:
   SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift
Log:
 

Modified: SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift	2013-10-28 18:57:59 UTC (rev 7238)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift	2013-10-28 19:09:37 UTC (rev 7239)
@@ -4,7 +4,6 @@
 type query;
 
 type script;
-type exec;
 
 type headerfile;
 type indexfile;
@@ -54,8 +53,8 @@
 }
 
 string num_partitions = arg("n", "10");
-fastaseq partition[] <ext;exec = "examples/splitmapper.sh", n = num_partitions>;
-database formatdbout[] <ext; exec = "examples/formatdbmapper.sh", n = num_partitions>;
+fastaseq partition[] <ext;exec = "examples/blast/splitmapper.sh", n = num_partitions>;
+database formatdbout[] <ext; exec = "examples/blast/formatdbmapper.sh", n = num_partitions>;
 
 script map_wrapper    <"map_wrapper.sh">;
 script red_wrapper    <"reduce_wrapper.sh">;
@@ -63,14 +62,11 @@
 script map_func       <"examples/blast/map_blast.sh">;
 script red_func       <"examples/reduce_sort.sh">;
 
-exec exeblastall <"examples/blastall">;
-exec exeblastmerge <"examples/blastmerge">;
-
 fileptr map_out[] <simple_mapper; prefix="map", suffix=".out">;
 file  map_err[] <simple_mapper; prefix="map", suffix=".err">;
 
 fastaseq dbin <single_file_mapper;file = arg("d", "/home/maheshwari/Swift-MapRed/blast/nr")>;
-query query_file <single_file_mapper;file = arg("i", "sequence.seq")>;
+query query_file <single_file_mapper;file = arg("i", "examples/blast/sequence.seq")>;
 
 partition=split_database(dbin, num_partitions);
 

Added: SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/sequence.seq
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/sequence.seq	                        (rev 0)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/sequence.seq	2013-10-28 19:09:37 UTC (rev 7239)
@@ -0,0 +1,106 @@
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