[Bioperl-l] Fwd: having problems with abi.pm

[Aaron J. Mackey]

I'm stumped on this one ...


> From: "Pinar Kondu" <pkondu at yahoo.com>
> Date: Tue Oct 7, 2003  12:03:02 PM US/Eastern
> To: "Aaron J. Mackey" <amackey at pcbi.upenn.edu>
> Subject: Re: having problems with abi.pm
>
> Hi again Aaron,
>
> It looks like it is working now, but I received an error message in 
> read.pm
> Since I assume I am not supposed to make any modifications in the 
> modules, I
> wanted to ask you what this message means:
>
> Here is how I ran my program:
> [root at iontek pinarperl]# perl test2.pl -a
> /home/ORTAKSKY/SEQUENCES/myfile.abi -p 
> /home/ORTAKSKY/SEQUENCES/myfileout
>
> Here is the message I got:
> Can't use an undefined value as filehandle reference at
> /usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/staden/read.pm line 115.
>
> The script is below.
>
> many thanks! -pinar
>
>
>>>>>>>
>>>>>>> #!/usr/bin/perl -w
>>>>>>>
>>>>>>> use strict;
>>>>>>> use Bio::SeqIO;
>>>>>>> use Getopt::Std;
>>>>>>>
>>>>>>> my %args;
>>>>>>> getopt("ap", \%args);
>>>>>>> if (!$args{a}) {
>>>>>>>   die "Please specify the input ABI file name!";
>>>>>>> }
>>>>>>> if (!$args{p}) {
>>>>>>>   die "Please specify the output PHD file name!";
>>>>>>> }
>>>>>>>
>>>>>>> my $ABIin = new Bio::SeqIO( -format => "ABI", -file => "$args{a}"
>>>>>>> );
>>>>>>>
>>>>>>> my $PHDout = new Bio::SeqIO( -format => "phd", -file =>
>>>>>>> ">$args{p}" );
>>>>>>>
>>>>>>> while (my $seq = $ABIin->next_seq) {
>>>>>>>     $PHDout->write_seq($seq);
>>>>>>> }
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>