[Bioperl-l] Bio::DB::DBFetch question
Sean O'Keeffe
seanok at gsf.de
Thu May 27 11:23:40 EDT 2004
Hi There,
I'm trying to convert a list of genbank/est ids to fasta sequences. I
want to use the Bio::DB::DBFetch module.
Script I have written/plagiarised is as follows:
#!/usr/bin/perl
use lib "/usr/local/ensembl-20/bioperl-live";
use Bio::DB::DBFetch;
use Bio::SeqIO;
open (IN, "est-id.txt") || die "can't open input file $! \n"; # get
filehandle to file containing list of id's
my $db = Bio::DB::DBFetch->new(); # make a new connection to DBFetch
my $seqio = $db->get_Stream_by_id(<IN>); # get stream obj using
filehandle
my $out = Bio::SeqIO->new(-file => ">est-id.fa", -format => 'Fasta');
# specify output format
while ( my $seq = $seqio->next_seq() ) {$out->write_seq($seq); } # do
the conversion
Error to stdout is as follows:
"Can't use string ("") as a HASH ref while "strict refs" in use at
/usr/local/ensembl-20/bioperl-live/Bio/DB/DBFetch.pm line 286, <IN> line
4515188."
I've used the filename, filehandle (as shown) as well as an array
reference to the id list.
A sample of the file list is below
AA000575
AA001887
AA002222
AA003931
AA004784
AA009419
AA009723
AA010084
AA010160
AA010193
AA010220
AA010230
AA012989
AA014259
AA018136
AA018184
AA018858
AA019868
AA020505
AA022701
AA023333
Can anyone open my eyes?
Thanks,
Sean.
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