From 271e2c0faa3f7bfb87563c5156bccb8f87f9478b Mon Sep 17 00:00:00 2001
From: elserj <elserj@localhost>
Date: Tue, 22 Sep 2009 19:41:47 +0000
Subject: [PATCH] Fixed the file so it wasn't a symlink

svn path=/; revision=8
---
 .../inparanoid_output_parse.pl                | 166 ++++++++++++++++++
 1 file changed, 166 insertions(+)
 create mode 100755 interactome_scripts/inparanoid_output_parse.pl

diff --git a/interactome_scripts/inparanoid_output_parse.pl b/interactome_scripts/inparanoid_output_parse.pl
new file mode 100755
index 0000000..be7f965
--- /dev/null
+++ b/interactome_scripts/inparanoid_output_parse.pl
@@ -0,0 +1,166 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use DBI;
+use Term::Screen::ReadLine;
+
+# open the file to be parsed, assume this is all sqltable* files in directory
+
+my @files = glob("sqltable*");
+
+# define the database handle to be used 
+
+my $screen = Term::Screen::ReadLine->new();
+	# clear the screen
+	$screen->clrscr;
+	# ask for username
+	$screen->at(0,0)->puts("Username: ");
+	my $username = $screen->readline(ROW => 0, COL=>11);
+
+	# ask for password, replace character presses with stars
+	$screen->at(1,0)->puts("Password: ");
+	my $password = $screen->readline(ROW => 1, COL => 11, PASSWORD => 1);
+
+	$screen->at(2,0);
+	undef $screen;
+	
+my $dbh = DBI->connect('DBI:mysql:inparanoid_data;host=floret.cgrb.oregonstate.edu', $username, $password,
+	{ RaiseError=> 1, AutoCommit=>1 }
+	) or die "Failed to connect to database: $DBI::errstr";
+	
+	
+# start the database entries
+foreach my $input_file (@files) {
+	open(in_file, "$input_file") || die "Error: file '$input_file' can not be opened\n";
+
+	my %clust_hash;
+
+	
+
+	my ($species_1, $species_2) = split("-", $input_file);
+	$species_1 = find_species($species_1);
+	$species_2 = find_species($species_2);
+	my $species_table = $species_1."_".$species_2;
+	my $clust_table = "clusters";
+
+	my %id_hash;
+
+
+	
+		
+		my $safe_species_table = $dbh->quote_identifier($species_table);
+		$dbh->do("drop table if exists $safe_species_table");
+		$dbh->do("CREATE TABLE $safe_species_table (
+			`id` INT( 11 ) NOT NULL ,
+			`bit_score` INT( 11 ) NOT NULL ,
+			`species` VARCHAR( 255 ) NOT NULL ,
+			`score` FLOAT( 11 ) NOT NULL ,
+			`gene` VARCHAR( 255 ) NOT NULL ,
+			INDEX ( `id` )
+			) TYPE = MYISAM");
+		my $sth = $dbh->prepare("insert into $safe_species_table (id, bit_score, species, score, gene) values (?,?,?,?,?)");
+	
+	
+		my $safe_clust_table = $dbh->quote_identifier($clust_table);
+		my $sth_id_dump = $dbh->prepare("select * from clusters");
+		my $sth_id_add = $dbh->prepare("insert into $safe_clust_table (id, clust_id) values (?,?)");
+		my $sth_get_id = $dbh->prepare("select last_insert_id(id) from clusters order by id desc limit 1");
+	
+		# put the clusters table data into a hash
+		$sth_id_dump->execute();
+		while(my @ids = $sth_id_dump->fetchrow_array) {
+			if(!defined($id_hash{$ids[1]})) {
+				$id_hash{$ids[1]} = $ids[0];
+			}
+		}
+	
+	my $clust_id_prev = "";
+
+	while(<in_file>) {
+		my $entry = $_;
+		# strip off newline characters
+		$entry =~ s/\r//g;
+		$entry =~ s/\n//g;
+	
+		my $id;
+	
+		my ($clust_id, $bit_score, $species, $score, $gene_header) = split ("\t", $entry);
+	
+		$clust_id = "$species_1"."___".$species_2."___".$clust_id;
+		$species = find_species($species);
+	
+		if(!defined($id_hash{$clust_id})) {
+			if ($clust_id ne $clust_id_prev) {
+				$sth_id_add->execute(undef, $clust_id);
+			
+				$sth_get_id->execute();
+				my @new_id = $sth_get_id->fetchrow_array;
+				$id = $new_id[0];
+				$id_hash{$clust_id} = $id;
+			}
+		}else {
+			$id = $id_hash{$clust_id};
+		}
+	
+		$sth->execute($id, $bit_score, $species, $score, $gene_header);
+	
+		$clust_id_prev = $clust_id;
+
+		
+	}
+	$sth_get_id->finish();
+}
+
+
+$dbh->disconnect;
+	
+
+sub find_species {
+	my $temp = $_[0];
+	if ($temp =~ /Arabidopsis/) {
+		$temp = "Ath";
+	}elsif ($temp =~ /brachypodium/) {
+		$temp = "Brachy";
+	}elsif ($temp =~ /elegans/) {
+		$temp = "C_elegans";
+	}elsif ($temp =~ /Chlamy/) {
+		$temp = "Chlamy";
+	}elsif ($temp =~ /Danio/) {
+		$temp = "Danio";
+	}elsif ($temp =~ /E\_coli/) {
+		$temp = "E_coli";
+	}elsif ($temp =~ /Glycine/) {
+		$temp = "Soy";
+	}elsif ($temp =~ /Homo\_sapiens/) {
+		$temp = "Human";
+	}elsif ($temp =~ /Maize/) {
+		$temp = "Maize";
+	}elsif ($temp =~ /musculus/) {
+		$temp = "Mouse";
+	}elsif ($temp =~ /neurospora/) {
+		$temp = "Neurospora";
+	}elsif ($temp =~ /Oryza\sativa/) {
+		$temp = "Oryza_sativa";
+	}elsif ($temp =~ /Physcomit/) {
+		$temp = "Physcomitreall";
+	}elsif ($temp =~ /cerevisiae/) {
+		$temp = "Sacc_cerevisiae";
+	}elsif ($temp =~ /pombe/) {
+		$temp = "Sacc_pombe";
+	}elsif ($temp =~ /Selaginella/) {
+		$temp = "Selaginella";
+	}elsif ($temp =~ /Sorghum/) {
+		$temp = "Sorghum";
+	}elsif ($temp =~ /Synechosystis/) {
+		$temp = "Synechosystis";
+	}elsif ($temp =~ /Vitis\_vinifera/) {
+		$temp = "Grape";
+	}else {
+		die "Error: Species can not be found from file name!";
+	}
+	return $temp;
+}
+
+
-- 
2.34.1