From 7a87356d6708ad97679be4475071cee3f804e597 Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 16 Dec 2014 23:46:49 +0000
Subject: [PATCH] Scripts that can be used together to run inParanoid as an SGE
 batch array style job, also removes files after completion except for
 sqltable files which is moved to sqltables directory

svn path=/; revision=598
---
 interactome_scripts/create_fasta_list.sh     | 18 ++++++++++++
 interactome_scripts/run_array_job_by_id.pl   | 31 ++++++++++++++++++++
 interactome_scripts/run_inparanoid_single.sh | 30 +++++++++++++++++++
 3 files changed, 79 insertions(+)
 create mode 100755 interactome_scripts/create_fasta_list.sh
 create mode 100755 interactome_scripts/run_array_job_by_id.pl
 create mode 100755 interactome_scripts/run_inparanoid_single.sh

diff --git a/interactome_scripts/create_fasta_list.sh b/interactome_scripts/create_fasta_list.sh
new file mode 100755
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]}" >> $outfile
+		((counter++))
+	done
+done
+
diff --git a/interactome_scripts/run_array_job_by_id.pl b/interactome_scripts/run_array_job_by_id.pl
new file mode 100755
index 0000000..4340cc4
--- /dev/null
+++ b/interactome_scripts/run_array_job_by_id.pl
@@ -0,0 +1,31 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+
+if($#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 $species_2\n";
+
+
diff --git a/interactome_scripts/run_inparanoid_single.sh b/interactome_scripts/run_inparanoid_single.sh
new file mode 100755
index 0000000..6b32d1b
--- /dev/null
+++ b/interactome_scripts/run_inparanoid_single.sh
@@ -0,0 +1,30 @@
+#!/bin/bash
+
+currentdir=(`pwd`)
+date=(`date +%m_%d_%y`)
+directory=/lemma/inparanoid_data/$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
-- 
2.34.1