[Swift-commit] r7224 - SwiftApps/Swift-MapRed/blast
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Thu Oct 24 14:39:33 CDT 2013
Author: ketan
Date: 2013-10-24 14:39:33 -0500 (Thu, 24 Oct 2013)
New Revision: 7224
Added:
SwiftApps/Swift-MapRed/blast/blast.c++.swift
Modified:
SwiftApps/Swift-MapRed/blast/blast.swift
SwiftApps/Swift-MapRed/blast/cf
SwiftApps/Swift-MapRed/blast/sites.xml
SwiftApps/Swift-MapRed/blast/tc.data
Log:
blast working
Added: SwiftApps/Swift-MapRed/blast/blast.c++.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.c++.swift (rev 0)
+++ SwiftApps/Swift-MapRed/blast/blast.c++.swift 2013-10-24 19:39:33 UTC (rev 7224)
@@ -0,0 +1,59 @@
+
+type fastaseq;
+type headerfile;
+type indexfile;
+type seqfile;
+type query;
+type output;
+
+type database {
+ headerfile phr;
+ indexfile pin;
+ seqfile psq;
+}
+
+string num_partitions = arg("n", "50");
+
+string program_name = arg("p", "blastp");
+
+fastaseq dbin <single_file_mapper;file = arg("d", "nr")>;
+
+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;
+}
+
+app (database out) formatdb (fastaseq i){
+ formatdb "-dbtype" "prot" "-in" @filename(i);
+ }
+
+app (output o) blastapp(query i, fastaseq d, string e, string f, database db){
+ blastp "-query" @filename(i) "-out" @filename(o) "-db" @filename(d) "-evalue" e "-html" "-outfmt" "1";
+}
+
+app (output o) blastmerge(output o_frags[]){
+ blastmerge filename(o) filenames(o_frags);
+}
+
+
+partition=split_database(dbin, num_partitions);
+
+foreach part,i in partition {
+ formatdbout[i] = formatdb(part);
+ out[i] = blastapp(query_file, part, expectation_value, filter_query_sequence, formatdbout[i]);
+}
+
+blast_output_file = blastmerge(out);
Modified: SwiftApps/Swift-MapRed/blast/blast.swift
===================================================================
--- SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/blast.swift 2013-10-24 19:39:33 UTC (rev 7224)
@@ -1,59 +1,55 @@
-
type fastaseq;
type headerfile;
type indexfile;
type seqfile;
-type query;
-type output;
-
-type database {
+type database
+{
headerfile phr;
indexfile pin;
seqfile psq;
}
-string num_partitions = arg("n", "50");
+type query;
+type output;
-string program_name = arg("p", "blastp");
+string num_partitions=@arg("n", "8");
+string program_name=@arg("p", "blastp");
+fastaseq dbin <single_file_mapper;file=@arg("d", "nr")>;
+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 dbin <single_file_mapper;file = arg("d", "nr")>;
+fastaseq partition[] <ext;exec="splitmapper.sh",n=num_partitions>;
-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;
+app (fastaseq out[]) split_database (fastaseq d, string n)
+{
+ fastasplitn @filename(d) n;
}
-app (database out) formatdb (fastaseq i){
- formatdb "-i" filename(i);
+app (database out) formatdb (fastaseq i)
+{
+ formatdb "-i" @filename(i);
}
-app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db){
- blastall "-p" p "-i" filename(i) "-d" filename(d) "-o" filename(o) "-e" e "-T" "-F" f;
+app (output o) blastapp(query i, fastaseq d, string p, string e, string f, database db)
+{
+ blastall "-p" p "-i" @filename(i) "-d" @filename(d) "-o" @filename(o) "-e" e "-T" "-F" f;
}
-app (output o) blastmerge(output o_frags[]){
- blastmerge filename(o) filenames(o_frags);
+app (output o) blastmerge(output o_frags[])
+{
+ blastmerge @filename(o) @filenames(o_frags);
}
-
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]);
+ out[i]=blastapp(query_file, part, program_name, expectation_value, filter_query_sequence, formatdbout[i]);
}
-blast_output_file = blastmerge(out);
+blast_output_file=blastmerge(out);
Modified: SwiftApps/Swift-MapRed/blast/cf
===================================================================
--- SwiftApps/Swift-MapRed/blast/cf 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/cf 2013-10-24 19:39:33 UTC (rev 7224)
@@ -3,7 +3,7 @@
file.gc.enabled=false
status.mode=provider
execution.retries=0
-lazy.errors=false
-use.provider.staging=true
+lazy.errors=true
+use.provider.staging=false
provider.staging.pin.swiftfiles=true
use.wrapper.staging=false
Modified: SwiftApps/Swift-MapRed/blast/sites.xml
===================================================================
--- SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/sites.xml 2013-10-24 19:39:33 UTC (rev 7224)
@@ -5,7 +5,7 @@
<profile namespace="karajan" key="jobThrottle">0.06</profile>
<profile namespace="karajan" key="initialScore">10000</profile>
<filesystem provider="local"/>
- <workdirectory>swift.work</workdirectory>
+ <workdirectory>/scratch/local/maheshwari/swift.work</workdirectory>
<profile namespace="swift" key="stagingMethod">local</profile>
</pool>
</config>
Modified: SwiftApps/Swift-MapRed/blast/tc.data
===================================================================
--- SwiftApps/Swift-MapRed/blast/tc.data 2013-10-24 16:25:39 UTC (rev 7223)
+++ SwiftApps/Swift-MapRed/blast/tc.data 2013-10-24 19:39:33 UTC (rev 7224)
@@ -1,4 +1,6 @@
-localhost blastall /opt/local/bin/blastall
-localhost fastasplitn /Users/ketan/Swift-MapRed/blast/parallelblast_2.0.9/fastasplitn
-localhost blastmerge /Users/ketan/Swift-MapRed/blast/parallelblast_2.0.9/blastmerge
-localhost formatdb /opt/local/bin/formatdb
+localhost blastp /home/maheshwari/ncbi-blast-2.2.28+/bin/blastp
+localhost fastasplitn /home/maheshwari/parallelblast_2.0.9/fastasplitn
+localhost blastmerge /home/maheshwari/parallelblast_2.0.9/blastmerge
+#localhost formatdb /home/maheshwari/ncbi-blast-2.2.28+/bin/makeblastdb
+localhost blastall /home/maheshwari/blast-2.2.26/bin/blastall
+localhost formatdb /home/maheshwari/blast-2.2.26/bin/formatdb
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