From 63f40215b3a73bb0a2e22774f6e3c26bb1c3dbf3 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 22 Feb 2011 04:17:36 +0000
Subject: [PATCH] 2 more scripts I found helpful in syncing (and cleaning up)
 the 1000G mirror

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5287 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/sync1000Genomes/checkMD5s.pl             | 43 +++++++++++++++++++
 .../findFilesNotInAlignmentIndex.sh           |  6 +++
 2 files changed, 49 insertions(+)
 create mode 100755 perl/sync1000Genomes/checkMD5s.pl
 create mode 100755 perl/sync1000Genomes/findFilesNotInAlignmentIndex.sh

diff --git a/perl/sync1000Genomes/checkMD5s.pl b/perl/sync1000Genomes/checkMD5s.pl
new file mode 100755
index 000000000..199b2d04b
--- /dev/null
+++ b/perl/sync1000Genomes/checkMD5s.pl
@@ -0,0 +1,43 @@
+#!/usr/bin/perl -w
+
+use Getopt::Long;
+
+sub usage {
+    print "Usage: perl checkMD5s.pl\n\t-ai <alignment.index to check>\n\t-o <file to store results>\n";
+    exit(1);
+}
+
+
+my $ai = undef;
+my $out = undef;
+GetOptions( "ai=s" => \$ai,
+	    "o=s" => \$out);
+
+usage() if ( !$ai || !$out );
+
+open(OUT, "> $out") or die "can't open $out: $!";
+
+open(LIST, "< $ai") or die "can't open $ai: $!";
+while ( <LIST> ) {
+    @pieces = split(' ', $_);
+    if ( @pieces == 6 ) {
+	check($pieces[0], $pieces[1]);
+	check($pieces[2], $pieces[3]);
+	check($pieces[4], $pieces[5]);
+    }
+}
+
+close(LIST);
+close(OUT);
+
+sub check {
+
+    my $file = $_[0];
+    my $target = $_[1];
+
+    print "Checking /humgen/1kg/DCC/ftp/$file\n";
+    @md5 = split(' ', `md5sum /humgen/1kg/DCC/ftp/$file`);
+    if ( $md5[0] ne $target ) {
+	print OUT "$file\t$md5[0]\t$target\n";
+    }
+}
diff --git a/perl/sync1000Genomes/findFilesNotInAlignmentIndex.sh b/perl/sync1000Genomes/findFilesNotInAlignmentIndex.sh
new file mode 100755
index 000000000..1592b1fff
--- /dev/null
+++ b/perl/sync1000Genomes/findFilesNotInAlignmentIndex.sh
@@ -0,0 +1,6 @@
+#!/bin/bash
+find /humgen/1kg/DCC/ftp/data/ -type f | awk -F "/" '{print $6 "/" $7 "/" $8 "/" $9}' | sort > filesWeHave.list
+grep -v MD5 /humgen/1kg/DCC/ftp/alignment.index | awk '{print $1 "\n" $3 "\n" $5}' | sort > filesWeWant.list
+comm -23 filesWeHave.list filesWeWant.list > filesToDelete.list
+comm -13 filesWeHave.list filesWeWant.list > filesToGet.list
+