Scripts that can be used together to run inParanoid as an SGE batch array style job...

svn path=/; revision=598

diff --git a/interactome_scripts/create_fasta_list.sh b/interactome_scripts/create_fasta_list.sh
new file mode 100755 (executable)
index 0000000..08f5988
--- /dev/null
+++ b/interactome_scripts/create_fasta_list.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+outfile="fasta_job_list.txt"
+
+counter=1
+
+lsarray=(`ls *.fa`)
+len=${#lsarray[@]}
+
+for (( i=0; i<$len; i++))
+do
+        for (( j=$i+1; j<$len; j++ ))
+        do
+               echo "$counter  ${lsarray[$i]}  ${lsarray[$j]}" >> $outfile
+               ((counter++))
+       done
+done
+

diff --git a/interactome_scripts/run_array_job_by_id.pl b/interactome_scripts/run_array_job_by_id.pl
new file mode 100755 (executable)
index 0000000..4340cc4
--- /dev/null
+++ b/interactome_scripts/run_array_job_by_id.pl
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+
+if($#ARGV != 1) {
+       print "usage: run_array_job_by_id.pl job_id id_mapping_file\n";
+       exit;
+}
+
+my $id = $ARGV[0];
+my $mappingFile = $ARGV[1];
+
+my %map_hash;
+
+open(MAPFILE, "$mappingFile");
+while(<MAPFILE>) {
+               my $line = $_;
+               chomp $line;
+               my ($map_id, $species_1, $species_2) = split(/\s+/, $line);
+               $map_hash{$map_id} = "$species_1\t$species_2";
+}
+
+close(MAPFILE);
+
+my ($species_1, $species_2) = split(/\s+/, $map_hash{$id});
+
+system "run_inparanoid_single.sh $species_1 $species_2\n";
+
+

diff --git a/interactome_scripts/run_inparanoid_single.sh b/interactome_scripts/run_inparanoid_single.sh
new file mode 100755 (executable)
index 0000000..6b32d1b
--- /dev/null
+++ b/interactome_scripts/run_inparanoid_single.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+currentdir=(`pwd`)
+date=(`date +%m_%d_%y`)
+directory=/lemma/inparanoid_data/$date
+mkdir -p $directory
+
+file1=$1
+file2=$2
+
+dirname=$directory/${file1}_______${file2}
+mkdir -p $dirname
+fasta_header_fix.pl ${file1} $dirname/${file1}
+fasta_header_fix.pl ${file2} $dirname/${file2}
+cd $dirname
+cp /home/bpp/elserj/Orthology_software/inparanoid/inparanoid_fixed.pl ./
+cp /home/bpp/elserj/Orthology_software/inparanoid/blast_parser.pl ./
+cp /home/bpp/elserj/Orthology_software/inparanoid/BLOSUM62 ./
+cp /home/bpp/elserj/Orthology_software/inparanoid/InparanoidXMLCreator.pl ./
+cp /home/bpp/elserj/Orthology_software/inparanoid/seqstat.jar ./
+
+cp /lemma/inparanoid_data/07_22_14/sqltables/sqltable.Triticum_urartu_gramene_ftp_1_17_14.fa-Zea_mays_phytozome_mart_9_9_13.fa ./
+
+inparanoid_fixed.pl ${file1} ${file2}
+
+mkdir -p $directory/sqltables
+mv sqltable.${file1}-${file2} $directory/sqltables
+
+cd ..
+rm -r $dirname