[Swift-commit] r2807 - usertools/cio/science/blast

[noreply at svn.ci.uchicago.edu]

Author: aespinosa
Date: 2009-04-01 22:27:18 -0500 (Wed, 01 Apr 2009)
New Revision: 2807

Modified:
   usertools/cio/science/blast/blast.swift
   usertools/cio/science/blast/mapper-in.sh
   usertools/cio/science/blast/mapper-out.sh
Log:
Added the summarizer workflow.  Also swift seemed to change sorting sequences of file to what it should be.  thus the index of *.seq file is back to normal.

Modified: usertools/cio/science/blast/blast.swift
===================================================================
--- usertools/cio/science/blast/blast.swift	2009-04-01 22:09:29 UTC (rev 2806)
+++ usertools/cio/science/blast/blast.swift	2009-04-02 03:27:18 UTC (rev 2807)
@@ -9,30 +9,28 @@
   error err;
 }
 
-(BlastResult out) blastall(BlastQuery i, BlastDatabase db[]) {
-  app {
-    /*
-    blastall "-p" "blastp" "-F" "F" "-d" @filename(db[10]) 
-	    "-i" @filename(i) "-v" "300" "-b" "300" "-m8" 
-		"-o" @filename(out.out) stderr=@filename(out.err);
-     */
-    mockblast "-p" "blastp" "-F" "F" "-d" @filename(db[10]) 
-	    "-i" @filename(i) "-v" "300" "-b" "300" "-m8" 
-		"-o" @filename(out.out) stderr=@filename(out.err);
-  }
+type BlastSummary;
+
+app (BlastResult out) blastall(BlastQuery i, BlastDatabase db[]) {
+  /*
+  blastall "-p" "blastp" "-F" "F" "-d" @filename(db[0]) 
+  */
+  mockblast "-p" "blastp" "-F" "F" "-d" @filename(db[0]) 
+      "-i" @filename(i) "-v" "300" "-b" "300" "-m8" 
+      "-o" @filename(out.out) stderr=@filename(out.err);
 }
 
-BlastDatabase pir[] <filesys_mapper;location="/disks/ci-gpfs/swift/blast/pir", pattern="UNIPROT_for_blast_14.0.seq*">;
-BlastResult out[] <ext;exec="mapper-out.sh", a="10", b="20", d="0497">;
-BlastQuery input[] <ext;exec="mapper-in.sh", a="10", b="20", d="0497">;
+app (BlastSummary sum) summarize(BlastResult out[]){
+  cat @filenames(out.out) stdout=@sum;
+}
 
-BlastQuery in_test <"test.in">;
-BlastResult out_test <simple_mapper;prefix="test">;
+BlastDatabase pir[] <filesys_mapper;location="common", pattern="UNIPROT_for_blast_14.0.seq*">;
+BlastResult out[] <ext;exec="mapper-out.sh">;
+BlastQuery input[] <ext;exec="mapper-in.sh">;
 
-
-out_test = blastall(in_test, pir);
-/*
-foreach data ,i in input {
-  (out[i],err[i]) = blastall(data, pir);
+foreach data,i in input {
+  (out[i]) = blastall(data, pir);
 }
-*/
+
+BlastSummary sum <"summary.out">;
+sum = summarize(out);

Modified: usertools/cio/science/blast/mapper-in.sh
===================================================================
--- usertools/cio/science/blast/mapper-in.sh	2009-04-01 22:09:29 UTC (rev 2806)
+++ usertools/cio/science/blast/mapper-in.sh	2009-04-02 03:27:18 UTC (rev 2807)
@@ -1,14 +1,18 @@
 #!/bin/bash
 
-while getopts ":a:b:d:" options; do
-  case $options in
-    a) export a=$OPTARG ;;
-	b) export b=$OPTARG ;;
-	d) export d=$OPTARG ;;
-	*) exit 1;;
-  esac
-done
+#while getopts ":a:b:d:" options; do
+#  case $options in
+#    a) export a=$OPTARG ;;
+#	b) export b=$OPTARG ;;
+#	d) export d=$OPTARG ;;
+#	*) exit 1;;
+#  esac
+#done
 
+export a=1
+export b=2
+export d=0000
+
 ls /disks/ci-gpfs/swift/blast/pir/input/$d/*.qry | \
   perl -wnl -e '$. >= $ENV{"a"} and $. <= $ENV{"b"}
     and print "[", $.-$ENV{"a"}, "] $_";'

Modified: usertools/cio/science/blast/mapper-out.sh
===================================================================
--- usertools/cio/science/blast/mapper-out.sh	2009-04-01 22:09:29 UTC (rev 2806)
+++ usertools/cio/science/blast/mapper-out.sh	2009-04-02 03:27:18 UTC (rev 2807)
@@ -1,13 +1,16 @@
 #!/bin/bash
 
-while getopts ":a:b:d:" options; do
-  case $options in
-    a) export a=$OPTARG ;;
-	b) export b=$OPTARG ;;
-	d) export d=$OPTARG ;;
-	*) exit 1;;
-  esac
-done
+#while getopts ":a:b:d:" options; do
+#  case $options in
+#    a) export a=$OPTARG ;;
+#	b) export b=$OPTARG ;;
+#	d) export d=$OPTARG ;;
+#	*) exit 1;;
+#  esac
+#done
+export a=1
+export b=2
+export d=0000
 
 ls /disks/ci-gpfs/swift/blast/pir/input/$d/*.qry | \
   perl -wnl -e '$. >= $ENV{"a"} and $. <= $ENV{"b"}