[Bioperl-l] Fetching genbank sequences

S.Paul s.paul at surrey.ac.uk
Mon Jun 14 01:36:20 EDT 2004

Hi Everyone:

I am trying to access the list of sequences for alpha-synuclein in genbank format and when I try to run the program, I get the following error(warning) message and the output file is not generated:

C:\research\perl\perlcodes>perl alpha_synuclein.pl
Query string
Homo sapiens[Organism] AND

-------------------- WARNING ---------------------
TTT T 3'];  double-stranded cDNA was ligated to Eco RI adaptors (Pharmacia),  di
gested with Not I and cloned into the Not I and Eco RI sites of  the modified pT
7T3 vector. Library is normalized, and was constructed  by Bento Soares and M.Fa
tima Bonaldo."" into chunks of 57 chars or less - this tag won't print right


I am not sure how to fix this; I am enclosing the code:

 use strict;
 use Bio::DB::Query::GenBank;
 use Bio::SeqIO;
 use Bio::DB::GenBank;
 my $query_string = ('Homo sapiens[Organism] AND
 print "Query string \n",$query_string;
 print "\n";
 my $query = new Bio::DB::Query::GenBank(-db=>'nucleotide',
 my $seqio=new Bio::DB::GenBank->get_Stream_by_query($query);
  print "Number of results:\n", $query->count, "\n";
 #open a seqio handle for writing the outputfile in genbank
 my $outfile = new Bio::SeqIO(-format=>'genbank',
  while (my $s = $seqio->next_seq) {
 #write the gbk
If I do the same thing and try to retrieve in fasta format, it seems to run but does not generate any output file.  I also noticed that after I run the program it seems to create files in the file directory with ".filename.pl.swp".  Is it trying to use the memory of the operating system?

Thanks in advance for the help


Sujoy Paul, PRISE Centre, UniS, s.paul at surrey.ac.uk

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