[Bioperl-l] Bio:Seq $seq_obj->accession_number not returning accession number?

[Sam Al-Droubi]

The fasta format for this sequence AF410462 from NCBI looks like this
 
 
>gi|17066572|gb|AF410462.1|AF410462 Mus musculus PEM homeobox (Pem) gene, promoter region and partial cds
ATGCGTGTGGGCATGCGCTCATGCCCACTTGCTTGAGCACATGTGTGCTCACATGGACGTTAGAGGCAAC
TTTCAGGAGTTATTTTTTTCCCTTCTAACTTGAGTTCCTGGACCTCAGACTTGTATAATAGGTACTTTCC
CAACTTAAGTCTTACTGGCTCCAGGGTATCTGGTATACTCTTCTAGCCTCCAAGGGCAGCCACTCATGCT
TCTTCAGGTGTGAAGAGGTGAGCCAGATACAACGGTGGGAGGCAGTGTGCCCTCAGTGTGTAGACTCTTT
ATGCCCTTGGGGATTAGCGCCTCTAGCTGCCAGTCGGGTCTCTGGGTCCCTCCTGCTAAGGCCACTCTCG
TCATGGTTCCTCTTGTCCTGGTGAGCCATTACGACCCTCTCACTTCCTTGTGTTCTCTTCCCTGTGTTCT
CTCTCTGCTGCTGTGGCCATTCTAGCTCCCTGCACAGTCCTTCAAGCTCACCTCCTGCCTTCCGTGGACA
AGAGGAAGCACAAAGAATCATCCAGTATGTATGCTCATGGCATAAGGGGATCCTGGGGAAGGGCTGAAGC
CTGAGCCGGGCTGGTCAACAGAATCTCCCTCTCCCTAACTCCATCTCCCTCTCCTTCCCTCTTCCTCTCT
CTATCCCTCCCCCCTCTCTCCCCCCACCACCGCATGTTTTGGGTCAGCTGACTGCTCTAGCCTTGATGAG
ATATCTTCCCAGGAAGAGTTGGTGCTGACTGTACAGATTGAGTTAGAGGGAGGGAAGAAAGCTCCTGTTT
GATCACTGGAGATCTTTATGCCTAGCTACATGTCTTACCAAAGCCAGGGGAGTCAGCTGAGCTGTAACTG
GGCACCCTAAGTTCTGCACACCCACATGCCCATGAACTGTGTCCATCTTGCAAGCACATCGTGCTCATTA
CATCCCCAAACTGCTATCACTTGTGTACCCCAAAGGCTCGGCCCACAGGAACGTCCTGTGAGCAAATCAC
AAAGACCAGCTTAGGGCTGGAAACATTGTAACCTGAAGTAGGCCAGAGGAGATCCCTGCCAGGTTGAGCA
TCACAGATCTCATTCTGTTCCCGGGGACACCAGGGGCCCAAGCTCAGAATCTGCCGAAGCATAACTTCAT
CATTGATCCTATTCAGGGTATGGAAGCTGAGGGTTCCAGCCGCAAGGTCACCAGGCTACTCCGCCTGGGA
GTCAAGGAAG
 
 When I read this from a file as a sequence object using Bio::Seq I get accession_number unknow.  The 
 accession number is in the header of the fasta file.  Anyone knows why this happens. 
 
 My code looks like this:
 
 print "primary id is: ",$seq_obj->primary_id."\n";
 print "Description is ",$seq_obj->desc."\n";
 print "Accession Number is ",$seq_obj->accession_number."\n";
 
 Output looks like this:
 
 primary id is: gi|17066572|gb|AF410462.1|AF410462
 Description is Mus musculus PEM homeobox (Pem) gene, promoter region and partial cds
 Accession Number is unknown
 
 
 Thank you.
 
 
 


Sincerely, 
Sam Al-Droubi, M.S.
saldroubi at yahoo.com