Re: Trouble parsing text with bioperl


Paul Lalli wrote:
jeffcullis@xxxxxxxxx wrote:
Hi, just having some problems running the following bioperl script.
It's supposed to download all the sequences in a file using the gi
numbers. But when I run it it only downloads one sequence of the five
in each line of the file, and that's it. When I uncomment the commented
line, the five sequences are downloaded no problem! I've even printed
out each element of @gi_nums and they correspond to the correct numbers
so I have no idea why they aren't all being downloaded. Any help on
this would be great.

#!/usr/bin/perl -w
use Bio::DB::GenPept;
open GIS, "<gis_5" or die "Can't open gi file";
my $gb = new Bio::DB::GenPept();

while($line = <GIS>) {
@gi_nums = split(' ', $line);

This would make @gi_nums be one array containing (if you're right about
your data) five elements.

#@gi_nums = ["78096912", "78096910", "78096909", "78096907",
"78096905"];

This would make @gi_nums be one array containing one element. That one
element would be a reference to an array that contains five elements.


my $seqio = $gb->get_Stream_by_id(@gi_nums);

I have no experience with BioPerl, so I have no idea what data this
method is looking for. If your commented line "works", then I would
suggest making your uncommented line match it - make it an array
containing one reference to an array, rather than an array containing
five elements:

@gi_nums = [ split(' ', $line) ];

Paul Lalli

Thanks Paul, that one change made everything work. I still have no idea
why the method needs strange input like that.

.

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