[Bioperl-l] outfile question mark

Frank Schwach fs5 at sanger.ac.uk
Thu Jan 26 06:24:32 EST 2012


try

chomp $line;

after my $line =<STDIN>;
at the moment you are creating a filename with a new-line in it

Hope that helps

Frank



On 26/01/12 10:52, Jordi Durban wrote:
> 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!


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


More information about the Bioperl-l mailing list