[Bioperl-l] how to get specific sub-sequence from GenBank file with Bio::DB::GenBank
Juan Jovel
jovel_juan at hotmail.com
Sun Apr 15 03:27:57 UTC 2012
Hello All,
I want to get some subsequences from provirus sequences in the GenBank, I got the whole sequences with the script below. However, I want to get a specific sub-sequence, which appears in the GenBank files in the line: LTR 9091..9723
how can I modify my script to get only nts 9091-9723 (in this example), instead of the whole sequence.
Thanks a lot in advance!________________________HERE THE SCRIPT:
#!/usr/bin/perl -wuse strict;use Bio::DB::GenBank;use Bio::SeqIO;
chomp(my $infile = $ARGV[0]);open(IN, "$infile") or die "$!";my @ids = <IN>;
chomp(my $outfile = $ARGV[1]);
my $seqs_out = Bio::SeqIO -> new(-file => ">$outfile", -format => "fasta");
foreach my $entry(@ids){ print "$entry"; my $db = Bio::DB::GenBank->new; my $seq = $db->get_Seq_by_acc($entry); $seqs_out->write_seq($seq); }exit;
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