Trouble parsing text with bioperl
- From: jeffcullis@xxxxxxxxx
- Date: 28 Jun 2006 11:25:18 -0700
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);
#@gi_nums = ["78096912", "78096910", "78096909", "78096907",
"78096905"];
my $seqio = $gb->get_Stream_by_id(@gi_nums);
while( my $seq = $seqio->next_seq ) {
print "seq id is ", $seq->display_id, "\n";
}
}
The file "gis_5" has the following contents:
78096912 78096910 78096909 78096907 78096905
82653972 82653970 82653968 82653967 82653965
.
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