Bob Freeman | 21 Jun 01:27 2013

Bio::PrimarySeq obj?

Hoping for an easy answer on this…

Using Bio::DB::Fasta to retrive a seqobj with get_Seq_by_id. I can print the raw sequence with
seqobj->seq(), but when I try to change and set the raw sequence data (e.g. seqobj->seq("ACTT"), the
change is ignored (as evidenced when writing out to new FASTA file).

Looking under the hood with the Perl debugger, it appears that the object returned is a
Bio::PrimarySeq::FASTA, which points to the whole (indexed) FASTA file; not what I had expected.

Is the PrimarySeq obj that is returned immutable? If so, is there an easy way to 'copy' the object so that I can
change the sequence and then write this out to a different file?


Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

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