[Bioperl-l] Assignment problem :(

Kurt Gobain enrique_rulz at yahoo.com
Thu Jan 4 17:15:16 EST 2007


Thanx for the replys...As suggested b Florin...I m posting the prog which I
had done so far...
=======================================================================
use strict;
use warnings;

my $dir= "$ARGV[0]" or die "inadequate argument at command line use 
/users/***/***/biocomputing1/assignment\n";
my $database="$ARGV[1]" or die "inadequate argument at commandline use 
/databases/swissprot/swissprot\n" ;
my $file;
my ($i,$seq);
my $length=0;
open (OUTPUT,">result.fasta");
opendir (DIR,"$dir") or die "cannot open the specified directory\n";
foreach $file (readdir DIR)
{
	if ($file =~ /\.embl/)
	{
		open(FILE,"$dir/$file") or die "cannot open the specified file\n";
		#print ">$file\n";
		#print OUTPUT ">$file\n";
		while (<FILE>)
		{
			
				if (/^\s/)
				{
					my @array = split ('',$sequence);
					foreach my $fasta_seq (@array)
					{
						if ( $fasta_seq =~ /[A-Za-z]/)
						{
							$length++;
							print "$fasta_seq";
							print OUTPUT "$fasta_seq";
						}
					}				
		print"\n";
		print "length of fasta sequence is $length\n";
				}
		}
		my $fasta_seq=@_;
		for ($i=0,$i<6,$i++)
		{
		my $result="blastall -F T -p blastp -d $database -i result.fasta -o 
blastresult.data";
		system($result);
		}
	print "\n";
	print OUTPUT"\n";
}

close (DIR);
close (FILE);
=======================================================================

I am stuck on bit no 5..

""for each sequence print the swissprot name and code of its close
homologues to an HTML formatted file that can be viewed in a web browser.Is
it possible to extract the evalues for each hit & record them in the HTML
file""

I am told we need to use sum Bioperl Packages. like Bio::DB::SwissProt,
Bio::SeqIO;....It wud be great if any 1 can shed lighte on this....

Thanx in advance..
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