[Bioperl-l] Where could I find FISH Map information in mapview data or somewhere else?

[Heikki Lehvaslaiho]

Ole,

The internals of EnsMart are best decribed by word 'fluid' at the moment
and they will continue to be so for some months. Eventually, there will
be a clear java and perl API to it. It remains to be seen if there is a
need for separate bioperl modules accessing EnsMart or if the perl
modules from the Ensembl project, which builds on bioperl, will be
enough.

FYI, before anyone spends hours looking in vain: you can not access the
karyotype information from EnsMart.

	-Heikki


On Tue, 2003-07-01 at 10:28, ole.st at gmx.de wrote:
> Hi,
> 
> I had the same problem some days before. You can also get the locus
> information
> via EnsMart (http://www.ensembl.org/EnsMart/) and store it in a file.
> I wonder why it's not possible to get this data with Bioperl. 
> 
> Ole
> 
> 
> > 
> > Dear Snag Chul Choi,
> > 
> > There is nothing bioperl that would draw the chromosomes for you, but I
> > can show how to get the data. It involves taking the details from the
> > human Ensembl (http://www.ensembl.org/) database. I'll first show how
> > you can manually browse the information and then easily download the
> > data.
> > 
> > 1. Log into the public ensembl database using a mysql client.
> > 
> >    % mysql -uanonymous -h kaka.sanger.ac.uk
> > 
> > 2. 'show databases;' lists the them all, but the latest human
> >    core database can currently be activated by:
> > 
> >    mysql> use homo_sapiens_core_14_31;
> > 
> > 3. The data you need is in table 'karyotype'
> > 
> >    mysql> describe karyotype;
> > +---------------+------------------+------+-----+---------+-------+
> > | Field         | Type             | Null | Key | Default | Extra |
> > +---------------+------------------+------+-----+---------+-------+
> > | chromosome_id | int(10) unsigned |      | PRI | 0       |       |
> > | chr_start     | int(10)          |      |     | 0       |       |
> > | chr_end       | int(10)          |      |     | 0       |       |
> > | band          | varchar(40)      |      | PRI |         |       |
> > | stain         | varchar(40)      |      |     |         |       |
> > +---------------+------------------+------+-----+---------+-------+
> > 5 rows in set (0.01 sec)
> > 
> >     and looks like this:
> > 
> >     mysql> select * from karyotype limit 5;
> > +---------------+-----------+----------+--------+--------+
> > | chromosome_id | chr_start | chr_end  | band   | stain  |
> > +---------------+-----------+----------+--------+--------+
> > |             1 |         0 |  2200000 | p36.33 | gneg   |
> > |             1 |   2200000 |  5100000 | p36.32 | gpos25 |
> > |             1 |   5100000 |  6900000 | p36.31 | gneg   |
> > |             1 |   6900000 |  8900000 | p36.23 | gpos25 |
> > |             1 |   8900000 | 12200000 | p36.22 | gneg   |
> > +---------------+-----------+----------+--------+--------+
> > 5 rows in set (0.03 sec)
> > 
> > 5. Since you are now connected to a remote host where you have not write
> > privileges, you can not save data. Log out.
> > 
> >    mysql> exit
> > 
> > 6. Run this from the command line:
> > 
> >   % mysql -uanonymous -h kaka.sanger.ac.uk -e \
> >     'select * from karyotype' homo_sapiens_core_14_31 \
> >     > karyotype.tab
> > 
> > 
> > If you do not have a suitable mysql client and can not get the data, let
> > me know and I'll mail the karyotype.tab file to you.
> > 
> > Yours,
> > 	-Heikki
> > 
> > 
> > On Tue, 2003-07-01 at 08:01, Sang Chul Choi wrote:
> > > Dear bioperl GURU:
> > > 
> > > NCBI's mapview data is so useful: it has contig assembly data, gene
> > data, etc.
> > > There is also FISH map information in "cyto_clone.md" file.
> > 
> > > However, I could not find out how ideogram could be painted. I wish I
> > could have 
> > > like these data:
> > > 
> > >             chromosome_start            chromosome_end
> > > 6p22.3  2000000                             3000000
> > > 6p22.2  3000001                             4000000
> > > 
> > > I would like to draw colorful chromosomes, how could I do that?
> > > 
> > > Thank you in advance.
> > > 
> > > Sincerely yours,
> > > 
> > > Sang Chul Choi
> > > 
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > -- 
> > ______ _/      _/_____________________________________________________
> >       _/      _/                      http://www.ebi.ac.uk/mutations/
> >      _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
> >     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
> >    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
> >   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
> >      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> > ___ _/_/_/_/_/________________________________________________________
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > 
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________