[Bioperl-l] using Bio::SeqIO to convert from table to genbank format ..... attribute_map example

[Cook, Malcolm]

Fellow long-time BioPerlers,

I am using Bio::SeqIO with success to convert between table (c.f.  http://search.cpan.org/~cjfields/BioPerl/Bio/SeqIO/table.pm) and genbank flatfile format.

I have Bio::SeqIO sequence format conversion wrapped in a command-line script.  The script exposes to the command line the parameters to ->new for both input and output objects through judicious use of GetOptions.  I have used this script in many conversion tasks between many different formats.

... except now ...

I am having trouble with reading the flatfile format.

Happily, at first, I see that -display_id and -accession_number are both parameters to Bio::SeqIO::table->new.  So they are naturally exposed to the command line as `in format=table header=1 display_id=1 seq=3"

Alas however -description is not a parameter to ->new.

The only way I can see to configure table.pm to take the sequence description (aka desc) from the 2nd column of my .tab file is as follows:

	$in->attribute_map({-description => 2});

... however my trace shows me that even though this does work to set the desc attribute of the wrapped Bio::Primary_seq to the value from column 2, unfortunately using the attribute_map also removes the individual values passed in for -display_id and -accession_number

Ideally (I think) Bio::SeqIO::table->new  would take a -description=2 instead of having to call attribute_map.  

Or, Bio::SeqIO::table->new  would take  -attribute_map and even accept it as a string which gets evaluated to a hash reference, just as I see -colnames can be passed as a string evaling to an array (which I see in the unit test: http://cpansearch.perl.org/src/CJFIELDS/BioPerl-1.6.924/t/SeqIO/table.t).  This would allow the hash to be supplied at the command line.

Or, am I missing something?

FWIW: I am trying to help a lab convert a few years of plasmids from DNAPlasmid to Genbank (for load into Vector NTI) and I am passing through Bio::SeqiO::table in-so-diong.....

Cheers, and Thanks for help and suggestions....

Malcolm Cook
Stowers Institute for Medical Research
1000 E 50th Street
Kanas City, MO 64110
(816) 926-4449
mec at stowers.org