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How can I use Bio::SeqIO to parse sequence data ... To see other biotech frequently asked questions,
please visit http://biotech.fyicenter.com/faq/
(Continued from previous question...) How can I use Bio::SeqIO to parse sequence data to or from a string? Use this code to parse sequence records from a string: use IO::String;
use Bio::SeqIO;
my $stringfh = new IO::String($string);
my $seqio = new Bio::SeqIO(-fh => $stringfh,
-format => 'fasta');
while( my $seq = $seqio->next_seq ) {
# process each seq
}
And here is how to write to a string: use IO::String; use Bio::SeqIO; my $s; my $io = IO::String->new(\$s); my $seqOut = new Bio::SeqIO(-format =>'swiss', -fh =>$io); $seqOut->write_seq($seq1); print $s; # $s contains the record in swissprot format and is stored in the string (Continued on next question...)
Other Frequently Asked Questions
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