[BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!!

[Moses M. Hohman]

Hi Zagato,

Why do you need to populate a BioSQL database, is the database an  
integration point with another BioSQL-compliant codebase?

I have limited BioRuby expertise (what I know I know from writing  
unit tests for BioRuby long ago, and reading over the codebase just  
now), but AFAIK BioRuby does not support BioSQL, nor does it support  
ASN.1. You can however parse that genome in the GenBank file format  
as follows:

genome = Bio::FlatFile.open(Bio::GenBank, "BA000002.gbk").entries[0]

That returns you a Bio::GenBank object, which has the following  
methods you can play around with:

["acc_version", "accession", "accessions", "basecount", "circular",  
"comment", "common_name", "date", "definition", "division",  
"each_cds", "each_gene", "entry_id", "exists?", "features", "fetch",  
"get", "gi", "keywords", "length", "locus", "nalen", "naseq",  
"natype", "nid", "organism", "origin", "references", "segment",  
"seq", "seq_len", "source", "strand", "tags", "taxonomy",  
"vernacular_name", "version", "versions"]

Hope that helps,

Moses

On Mar 9, 2007, at 6:53 AM, Zagato wrote:

> Thanks, it's a good start, for a newbie, but i still want to test,  
> so i test
> BioRuby Vs BioJava, and BioRuby is more faster :D and less harder  
> with the
> memory, i will try now with JRuby :-p, for enable JMS.
> In any case, i still want to know how to populate a BioSQL database  
> with
> Ruby automatically and if i can read an ASN.1 file to extract the  
> lineage.
>
> Lot of Thanks :D
>
> Alan Jairo Acosta
>
> On 3/8/07, Joel Dudley <jdudley at stanford.edu> wrote:
>>
>> You may find this link useful:
>>
>> http://sciruby.codeforpeople.com/sr.cgi/BioProjects
>>
>> - Joel
>>
>> On Mar 8, 2007, at 3:02 PM, Zagato wrote:
>>
>>> Hello, i'm trying to decide between BioJava and BioRuby for a work,
>>> but i'm
>>> a newbie, and doesn't exists a "table" that explanis what is the
>>> better
>>> choice an what are the differences :'(.
>>>
>>> By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with
>>> BioRuby to get
>>> lineage to poulate a BioSQL database on Postgres, is this
>>> posibble?, how?.
>>> Exists a form to load the BioSQL database from a .gbk, and asn
>>> Files from a
>>> genome automagicaly :-p ?
>>>
>>> Thanks and any help it's aprecciate.
>>>
>>> Alan Jairo Acosta
>>>
>>> --
>>> Farewell.
>>> http://www.youtube.com/zagatogekko
>>> ruby << __EOF__
>>>   puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
>>> __EOF__
>>> _______________________________________________
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>
>>
>
>
> -- 
> Farewell.
> http://www.youtube.com/zagatogekko
> ruby << __EOF__
>   puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
> __EOF__
> _______________________________________________
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>