[Swift-commit] r7159 - SwiftApps/Swift-MapRed/blast

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2013-10-14 16:10:47 -0500 (Mon, 14 Oct 2013)
New Revision: 7159

Modified:
   SwiftApps/Swift-MapRed/blast/blast.swift
   SwiftApps/Swift-MapRed/blast/tc.data
Log:
 


Modified: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift	2013-10-14 20:31:40 UTC (rev 7158)
+++ SwiftApps/Swift-MapRed/blast/blast.swift	2013-10-14 21:10:47 UTC (rev 7159)
@@ -2,27 +2,36 @@
 type headerfile;
 type indexfile;
 type seqfile;
+type query;
+type output;
 
-type database 
-{
+type database {
+
   headerfile phr;
   indexfile pin;
   seqfile psq;
 }
 
-type query;
-type output;
 
 string num_partitions=@arg("n", "8");
+
 string program_name=@arg("p", "blastp");
+
 fastaseq dbin <single_file_mapper;file=@arg("d", "database")>;
+
 query query_file <single_file_mapper;file=@arg("i", "sequence.seq")>;
+
 string expectation_value=@arg("e", "0.1"); 
+
 output blast_output_file <single_file_mapper;file=@arg("o", "output.html")>;
+
 string filter_query_sequence=@arg("F", "F");
 
 fastaseq partition[] <ext;exec="splitmapper.sh",n=num_partitions>;
 
+database formatdbout[] <ext; exec="formatdbmapper.sh",n=num_partitions>;
+output out[] <ext; exec="outputmapper.sh",n=num_partitions>;
+
 app (fastaseq out[]) split_database (fastaseq d, string n){
   fastasplitn @filename(d) n;
 }
@@ -41,9 +50,6 @@
 
 partition=split_database(dbin, num_partitions);
 
-database formatdbout[] <ext; exec="formatdbmapper.sh",n=num_partitions>;
-output out[] <ext; exec="outputmapper.sh",n=num_partitions>;
-
 foreach part,i in partition {
   formatdbout[i] = formatdb(part);
   out[i]=blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);

Modified: SwiftApps/Swift-MapRed/blast/tc.data
===================================================================
--- SwiftApps/Swift-MapRed/blast/tc.data	2013-10-14 20:31:40 UTC (rev 7158)
+++ SwiftApps/Swift-MapRed/blast/tc.data	2013-10-14 21:10:47 UTC (rev 7159)
@@ -1,27 +1,5 @@
-#This is the transformation catalog.
-#
-#It comes pre-configured with a number of simple transformations with
-#paths that are likely to work on a linux box. However, on some systems,
-#the paths to these executables will be different (for example, sometimes
-#some of these programs are found in /usr/bin rather than in /bin)
-#
-#NOTE WELL: fields in this file must be separated by tabs, not spaces; and
-#there must be no trailing whitespace at the end of each line.
-#
-# sitename  transformation  path   INSTALLED  platform  profiles
-localhost 	echo 		/bin/echo	INSTALLED	INTEL32::LINUX	null
-localhost 	cat 		/bin/cat	INSTALLED	INTEL32::LINUX	null
-localhost 	ls 		/bin/ls		INSTALLED	INTEL32::LINUX	null
-localhost 	grep 		/bin/grep	INSTALLED	INTEL32::LINUX	null
-localhost 	sort 		/bin/sort	INSTALLED	INTEL32::LINUX	null
-localhost 	paste 		/bin/paste	INSTALLED	INTEL32::LINUX	null
-localhost 	cp 		/bin/cp         INSTALLED	INTEL32::LINUX	null
-localhost 	touch 		/bin/touch      INSTALLED	INTEL32::LINUX	null
-localhost	wc		/usr/bin/wc	INSTALLED	INTEL32::LINUX	null
-localhost	sleep		/bin/sleep	null	null 	null
-localhost	blastall	/opt/local/bin/blastall		null		null		null
-localhost	fastasplitn	/Users/lgadelha/parallelblast/fastasplitn	null		null	null
-localhost	blastmerge	/Users/lgadelha/parallelblast/blastmerge	null		null	null
-localhost	formatdb	/opt/local/bin/formatdb							null		null	null
+localhost	blastall	/opt/local/bin/blastall	
+localhost	fastasplitn	/Users/lgadelha/parallelblast/fastasplitn 
+localhost	blastmerge	/Users/lgadelha/parallelblast/blastmerge 
+localhost	formatdb	/opt/local/bin/formatdb	
 
-