[Bioperl-l] Bio::Restriction::IO and REBASE file

Jelena Obradovic jelenaob at gmail.com
Fri May 26 12:47:05 EDT 2006


Hi there,

I have tried loading enzyme list from a file REBASE bairoch.605 using
Bio::Restriction::IO;

1. But for some reason the number of enzymes in the list is always 532
which is a default set of enzymes in enzyme collection.

Is there any known issue with this module or a workaround?

And here is the code I have been using:

my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-format=>"Bairoch")
|| die "can't load the file bairoch.605: $!";
my $enzymes = $re_in->read;
print "\nNo of enzymes: ", scalar $enzymes->each_enzyme, "\n";

2. The other problem is when trying to use format that is lower-case
it throws an exception, but when "B" is capitalized it is ok.
I assume it cannot load a file and does not initilize enzyme
collection properly.

Can't call method "each_enzyme" on an undefined value at
.../cgi-bin/seq-load.pl line 51.

Any thoughts?


Thanks in advance,


Jelena Obradovic
jelenaob at gmail.com



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