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

[ole.st at gmx.de]

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
> ___ _/_/_/_/_/________________________________________________________
> 
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> 

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