[Bioperl-l] outfile question mark

Jordi Durban jordi.durban at gmail.com
Thu Jan 26 05:52:31 EST 2012


Hi all!
I'm trying to parse a a balstxml file using a homemade script. When I run
the script the output file has a question mark and I don't know how to
avoid it as it's really painful to deal whit a unix command line.
Has anyone idea what I'm doing wrong??
That's what I used to try:
*
print "Waiting for a query name...\n";
my $line = <STDIN>;
open OUTFILE , ">".$line."-UTR.txt" or die "can't open outfile\n";
my $gb = Bio::DB::GenBank->new();
    print "Waiting for reference id...\n";
    my $gi = <STDIN>;
    chomp($gi);*

And I get a $file?-UTR.txt file.
Thanks a lot!
-- 
Jordi


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