Created; parses regulatory feature data from a cisRed database dump into a...

Created; parses regulatory feature data from a cisRed database dump into a file suitable for loading with load_regulatory.pl. Ideally load_regualatory.pl should be able to understand different file formats (with some command-line hint as to what it's looking it) and so remove the need for this intermediate step

misc-scripts/regulatory_regions/parse_cisred.pl

+# Parse regulatory feature data from a CisRED file into a file
+# in a format suitable for reading into an ensembl database using
+# load_regulatory.pl
+
+# Cisred data is available under http://www.cisred.org/files/Databases
+# e.g. http://www.cisred.org/files/Databases/cisREDdb-Hsap-1.1b/SQL/data.zip
+
+# File format of cisred features.txt file (tab separated)
+# id batch_id seqname source feature start end score strand frame ensembl_gene_id
+
+
+use strict;
+
+use DBI;
+use Getopt::Long;
+
+my ($infile, $outfile);
+
+GetOptions( "infile=s",   \$infile,
+	    "outfile=s",  \$outfile,
+	    "help",       \&usage);
+
+usage() if (!$infile || !$outfile);
+
+print "Reading from $infile\n";
+my $count = 0;
+
+open (INFILE,  "<$infile") || die "Can't open $infile";
+open (OUTFILE, ">$outfile") || die "Can't open $outfile";
+
+while (<INFILE>) {
+
+  my ($id,$batch_id,$seqname,$source,$feature,$start,$end,$score,$strand,$frame,$ensembl_gene_id) = split;
+
+  print OUTFILE join ("\t", "Similarity", $feature, $source, "transcription_factor", $seqname, $start, $end, $strand, $frame,$score,"gene","id","\"$ensembl_gene_id\"" ) . "\n";
+
+  # XXX transcription_factor?
+
+  $count++;
+
+}
+
+close INFILE;
+close OUTFILE;
+
+print "Wrote $count regulatory features to $outfile\n";
+
+sub usage {
+
+  print <<EOF;
+Usage: perl parse_cisred.pl
+         -infile    : Cisred features.txt file
+         -outfile   : File to be written for load_regulatory.pl
+
+Data files available from e.g.
+
+http://www.cisred.org/files/Databases/cisREDdb-Hsap-1.1b/SQL/data.zip
+
+EOF
+
+  exit(0);
+
+}