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

[Zagato]

I need BioSQL thinking that in the future other software can access to the
databse, and i belive that it's better use a Scheme Well-Defined. And the
other hand, i need read ASN.1 because contains <<lineage "Bacteria;
Acidobacteria; Acidobacteriales; Acidobacteriaceae",>> and i need this info
to organize in a tree the genome of bacterias, by now i thinking in use a
Regex to extract this.

Thanks for the tips.

Alan Jairo Acosta

On 3/13/07, Moses M. Hohman <mmhohman at northwestern.edu> wrote:
>
> 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
> >
>
>


-- 
Farewell.
http://www.youtube.com/zagatogekko
ruby << __EOF__
  puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse
__EOF__