[Bioperl-l] XML::DOM ?

Brian Osborne brian_osborne at cognia.com
Wed Jun 9 07:59:52 EDT 2004


This is difficult for me to comment on, in part because the error you're
getting now is different from the error you described in the last message,
so it seems that something has changed in your configuration, your script,
or in your files. Some suggestions, always show your code in your emails and
start to use perl's built-in debugger. Let's say you have a script that you
usually run like this:

>format.pl swiss.sp

To get into the deubugger do this:

>perl -d format.pl swiss.sp

Now step through your program line by line, using the "n" command. Examine
each and every variable to make sure it's what you think it should be, as in
"x $var". There are many more useful commands, there's also a useful
tutorial online at http://chicago.pm.org/meetings/20031202/perl-debug.txt.

Also, are you saying that there are no error messages when you do "perl -e
'use XML::DOM"? If there is an error message you need to show it to us.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of hafiz hafiz
Sent: Wednesday, June 09, 2004 12:08 AM
To: bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] XML::DOM ?

thank you to Brian Osborne .

i have done
>perl -e 'use XML::DOM'

and i have got new output but still can't transfer to

my output;

Enter filename for output

Enter format for output file:bsml

........Chance funtion.......
Can't call method "text" without a package or object
reference at
/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/bsml.pm line
1133, <GEN0> line 53.

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