Knowing The Status For Obsolete Refseq Entries

Question

[Woa]

I have a few thousand RefSeq IDs and some ( around a couple of 100s or so I guess) of them got obsolete. For example the entry XM_994796.2. Given the list of IDs I wish to know the IDs that have become obsolete. Any perl/python etc. snippet/script or API is much appreciated.

Thanks

Answer 1

[Woa]

I've tried this inside a loop

use  Bio::DB::RefSeq; 
    $db = Bio::DB::RefSeq->new(); 
    eval { $seq = $db->get_Seq_by_version('NM006732.1'); }; 
    print "accesion is ", $seq->accession_number, "\n" unless $@;

but it exits whenever it finds an obsolete entry breaking the loop and fails to look for all IDs.

Answer 2

[Woa]

Finally downloaded the data from the URL and parsed the files.

http://www.ncbi.nlm.nih.gov/nuccore/XM_994796.2?report=docsum&format=text

This works better as it shows if the sequence has been removed, updated , replaced by any other accession no. or remain unchanged.