This looks like a multi-fasta file holding DNA or protein sequence data (with sequence ID after the >). I use one of the following two ways to get this info into an array before piping into blast or other sequence manipulations.
The first is a loop from some hand-me-down code that works quite well (but any comments etc on optimization etc v. welcome...)
open( FASTAFILE, $ARGV[0] );
while (<FASTAFILE>) {
if ( /^>/ && $seqflag == 1 ) {
push ( @sequences, $fasta );
$fasta = "";
$fasta = $_;
}
elsif (/^>/) {
$fasta = $_;
$seqflag = 1;
}
else {
$fasta .= $_;
}
}
push ( @sequences, $fasta );
#then iterate @sequences to run over BLAST
The other (better?) way is the very nice
Bioperl modules that have methods that specifically handle multifasta flat files. Also check out
EMBOSS, a sequence analysis suite that interfaces with BioPerl...EMBOSS + BioPerl makes life sooo much easier...
From the
bioperl tutorial...
# script 1: create the index
use Bio::Index::Fasta; # using fasta file format
$Index_File_Name = shift;
$inx = Bio::Index::Fasta->new(
-filename => $Index_File_Name,
-write_flag => 1);
$inx->make_index(@ARGV);
# script 2: retrieve some files
use Bio::Index::Fasta;
$Index_File_Name = shift;
$inx = Bio::Index::Fasta->new($Index_File_Name);
foreach $id (@ARGV) {
$seq = $inx->fetch($id); # Returns Bio::Seq object
# do something with the sequence
}
Hope this helps,
tandemrepeat