Unfinished first effort at script.

Imports recombination maps.

misc-scripts/import_recombinant_hotspots.pl

+#!/usr/bin/env perl
+
+# Designed to work on data retrieved from 
+# ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110106_recombination_hotspots/
+#
+# Imports the recombination hotspots from 1000 Genomes into Ensembl
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Registry;
+use Bio::EnsEMBL::SimpleFeature;
+use Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Analysis;
+
+use Getopt::Long;
+use File::Fetch;
+use IO::Dir;
+use IO::File;
+
+my ($url,$db_name,$db_host,$db_user,$db_pass,$db_port,$db_version,$help,$species);
+$species = "human";
+
+GetOptions ("url=s" => \$url,
+            "db_name=s" => \$db_name,
+            "db_host=s" => \$db_host,
+            "db_user=s" => \$db_user,
+            "db_pass=s" => \$db_pass,
+            "db_port=s" => \$db_port,
+            "db_version=s" => \$db_version,
+            "species=s" => \$species,
+            "h!"        => \$help,
+            "help!"     => \$help,
+);
+
+if ($help) {&usage; exit;}
+unless ($url and $db_name and $db_host) {print "Insufficient arguments\n"; &usage; exit;}
+
+
+my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+    -species => $species,
+    -group => 'core',
+    -dbname => $db_name,
+    -host => $db_host,
+    -user => $db_user,
+    -pass => $db_pass,
+    -port => $db_port,
+    -db_version => $db_version,
+);
+
+Bio::EnsEMBL::Registry->add_DBAdaptor($species,'core',$dba);
+
+#Bio::EnsEMBL::Registry->load_registry_from_db(
+#    -host => $db_host,
+#    -user => $db_user,
+#    -pass => $db_pass,
+#    -port => $db_port,
+#    -db_version => $db_version,
+#);
+
+my $file_fetch = File::Fetch->new(uri=>$url);
+my $archive_path = $file_fetch->fetch() or die "Unable to get data from given URL. ".$file_fetch->error;
+
+system('tar','-xzf',$archive_path);
+
+my %directory;
+tie %directory, 'IO::Dir',".";
+foreach my $file (keys %directory) {
+    if ($file =~ /\.txt$/) {
+        my $fh = IO::File->new($file);
+        &process_file($fh);
+        $fh->close;
+    }
+}
+print "Finished. Feel free to delete downloaded data in this directory.\n";
+
+sub process_file {
+    my $file_handle = shift;
+    <$file_handle>; #strip header
+    
+    my $simple_feature_adaptor = Bio::EnsEMBL::Registry->get_adaptor($species,'core', 'SimpleFeature');
+    my $slice_adaptor = Bio::EnsEMBL::Registry->get_adaptor($species,'core', 'Slice');
+    
+    my $analysis = new Bio::EnsEMBL::Analysis (
+        -description => "The map was generated using the HapMap Phase II data and human genome assembly NCBI35 using LDhat as described in the 2007 HapMap paper (Nature, 18th Sept 2007).
+
+The map was then converted from NCBI35 to GRCh37 coordinates and inspected for regions in which
+the genome assembly had be rearranged.
+
+See ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20110106_recombination_hotspots/",
+        -display_label => 'HapMap Phase II genetic recombination map',
+        -displayable => 1,
+        -logic_name => 'INSERT SHORT NAME HERE',
+    );
+
+    my $previous_chromosome;
+    my $slice;
+    my @features;
+    while (my $line = <$file_handle>) {
+        my ($chromosome,$position,$score) = split(/\t+/,$line);
+        $chromosome =~ s/^chr//;  # chr prefix is for UCSC
+        $chromosome =~ s/\_.+$//; # for removing PAR info
+        if (!$slice || $previous_chromosome ne $chromosome) {
+            $slice = $slice_adaptor->fetch_by_region('toplevel', $chromosome);
+        }
+        my $simple_feature = Bio::EnsEMBL::SimpleFeature->new(
+            -start => $position,
+            -end => $position,
+            -score => $score,
+            -analysis => $analysis,
+            -slice => $slice,
+            -strand => 1,
+            -display_label => 'Recombination hotspot',
+        );
+        
+        push @features, $simple_feature;
+        $previous_chromosome = $chromosome;
+    }
+    $simple_feature_adaptor->store(@features);
+}
+
+sub usage {
+    print "Launching instructions:
+    Run from a folder you are happy to have filled with files.
+    
+Options:
+    
+    -url      Supply the URL to download from
+    -db_name  The DB to add these features to
+    -db_host  Hostname for the DB
+    -db_user
+    -db_pass
+    -db_port
+    -db_version
+    -species
+    
+    -help
+";    
+}
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