Re: [gmod-cmap] Help: Several Problems

[Ben F. <fag...@gm...>]

Hi Amy, 

Not sending large attachments to the mailing list is probably a good
idea.  I am going to send my response to the list though, since it might
be useful for someone searching the archive later. 

My responses are in-line:

On Sat, 2008-08-30 at 11:26 +0800, Lee Amy wrote:
> 1. When I import data, it shows following error messages:

> DBD::mysql::st execute failed: Duplicate entry 'GmComposite2003_J_Pod
> dehis 1-' for key 2 at /usr/lib/perl5/site_perl/5.8.
> 8/Bio/GMOD/CMap/Data/Generic.pm line 5124, <GEN5> line 4962.
> DBD::mysql::st execute failed: Duplicate entry 'GmComposite2003_J_Pod
> dehis 1-' for key 2
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data/Generic.pm line
> 5124, <GEN5> line 4962.

The problem is the feature_acc column size in the database.  The default
length is 30 characters.  Your feature_accs are getting cut off and thus
the duplicate entry error.

To fix this you can change the size of the *_acc column to a larger
number.  You may as well change map, map set and species while you are
at it.

The following commands work for changing the accessions in mysql.

alter table cmap_feature change column feature_acc feature_acc varchar(50) NOT NULL default '';
alter table cmap_map change column map_acc map_acc varchar(50) NOT NULL default ''; 
alter table cmap_map_set change column map_set_acc map_set_acc varchar(50) NOT NULL default '';
alter table cmap_species change column species_acc species_acc varchar(50) NOT NULL default '';



> 
> 2. Because of our usages, we have to put many feature_type parameters
> into the configuration file. So I wanna know how many colors I could
> use. In such case, I'm afraid that the colors are not enough. 

FOr a full list of available colors, take a look at
Bio/GMOD/CMap/Constants.pm.  Search for "COLORS" and you will find a
large list.

That should be enough but if it really isn't, I could add something to
CMap to let you specify an RGB value.

> 3. The last one is the format problem. In default, the map doesn't
> seem very pretty because the features and corresponding words mixed.
> It looks not clearly. So I suppose whether it's possible to change the
> style of showing maps. The picture I provide is my expected style. 

In the config file you can specify the corrs_to_map option.  Setting it
to 1 will cause the correspondences to be drawn to the map (as in your
picture) rather than to the features.

Basically, any options that you select to make a picture pretty, can be
set as defaults in the config file.

Hopefully that helps.

Ben