view galaxy-tools/tools/rdock/bin/sdfield @ 0:4eb3f9cb2a51 draft

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#!/usr/bin/perl 
# add extra fields to SD records
use lib "$ENV{'RBT_ROOT'}/lib";
use SDRecord;

printHelpAndExit() if (scalar(@ARGV) == 0);
#Parse command line arguments
my @files;
my $arg = shift @ARGV;
printHelpAndExit() if ($arg eq '-h');
#read records
my $sdRec = new SDRecord;
my $nRec=0;
# if not -h, then must be the FieldName
my $FieldName = $arg;
my $FieldVal  = shift @ARGV; # and this must be the filed value
# rest are the filenames
while ($sdRec->readRec('DATA'=>1,'LINES'=>1)) {
	$sdRec->addData('_REC' => ++$nRec);#add record# as temp data field
	$sdRec->addData('_FILE' => $ARGV);#add filename as temp data field
	$sdRec->addDataAndLines($FieldName => $FieldVal);
	$sdRec->writeRec();#write record
}

sub printHelpAndExit {
	print "\nAdding fields to SD files\n";
	print "Usage:\n";
	print "\tsdfield <Fieldname> <value> <infile[s]>\n";
	print "\t-h\tthis help\n";
	print "\t\n";
}