gmod-cmap — Discussion of the CMAP comparative map viewer

[gmod-cmap] Help: Cannot draw pictures

[Lee A. <ope...@gm...>]

Hello,

I have a data which contains 167 maps. And I can import it correctly but
when I draw the all maps, it seems that I cannot see these maps. I suppose
that whether that is too big to show, or any limitation I should change?

Huge thanks to you.

Best Regards,

Amy Lee

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

Re: [gmod-cmap] Help: No such pseudo-hash field "default_rank" at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap.pm line 234, <GEN5> line 153.

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

Hi Amy,

You have POSITION, QTL_1 and QTL_2 defined twice in the config file.  

Ben

On Thu, 2008-08-28 at 13:03 +0800, Lee Amy wrote:
> Hello,
> 
> I encountered a problem while I'm going to import data. When the
> cmap_admin.pl starts to do that an error shows by following words.
> 
> Importing map set data.
> Examining map set.
> 'TEST-YY' currently has 0 maps.
> Reading File.
> Parsing file...
> Created map F (103).
> No such pseudo-hash field "default_rank"
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap.pm line 234, <GEN5>
> line 304.
> 
> And at another machine that runs well. Anyway, I wonder something
> wrong such as Perl modules.
> 
> The attachments I provide are the data and configuration file.
> 
> Huge thanks~
> 
> Best Regards,
> 
> Amy
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Re: [gmod-cmap] Help: Bad index while coercing array into hash Problem

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

Hi,

Your configuration file has duplicate entries for the feature type
"marker".  Remove one of those and it should work.

Ben

On Mon, 2008-08-18 at 18:59 +0800, Lee Amy wrote:
> Ben,
> 
> I have solved the module/Perl problem I said before. Your module
> Bundle::CMap helps me a lot. I use it under the Perl 5.8.8 and import
> data correctly. Anyway, I encounter another problem while I use CMap
> to view maps. My CMap version is 1.01.
> 
> After importing data, when I choose "Shoe Selected Set's Maps", an
> error shows with following words:
> 
> Bad index while coercing array into hash
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Data.pm line 3899.
> 
> And any other options are unavailable. I feel a little confused
> because in my old machine when I fullfil the importing data task,
> everything goes well. So could you tell me how to solve this one? I
> attached the data file and configuration file.
> 
> Thank you very much~
> 
> Best Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
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Re: [gmod-cmap] Help: Correspondences Problem

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

When you created the correspondences, did it tell you that any had been
made?  There should be a line like the following in the output:

 Done, checked 156 map pairs, 52 corrs created/updated.

You can try using the matrix to see if they were created.

To do that use cmap_admin.pl and choose "Reload correspondence matrix".
Then go to the CMap web page and click on the matrix link at top.  Hit
submit on the form (or whatever the button is labeled) and it should
show you a table of correspondences.  

If that table is blank, then there are probably no correspondences in
the db.

Let us know how that goes.

Ben

On Thu, 2008-08-14 at 09:33 +0800, Lee Amy wrote:
> Hello,
> 
> I have set up three map sets and hope to draw the correspondences by
> the feature name automatically. I am following the "Automatic
> name-based correspondences" method to add the three map sets. After
> that, I use CMap to draw them when I add a right map it says "No maps
> available at these settings." I feel a little confused because I have
> add them by using cmap_admin.pl script.
> 
> Could you give me some tips?
> 
> Thank you very much~
> 
> Best Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
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[gmod-cmap] Help: Correspondences Problem

[Lee A. <ope...@gm...>]

Hello,

I have set up three map sets and hope to draw the correspondences by the
feature name automatically. I am following the "Automatic name-based
correspondences" method to add the three map sets. After that, I use CMap to
draw them when I add a right map it says "No maps available at these
settings." I feel a little confused because I have add them by using
cmap_admin.pl script.

Could you give me some tips?

Thank you very much~

Best Regards,

Amy Lee

Re: [gmod-cmap] Help: Permission Problem

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

Hi Amy Lee,

Can you do an "ls -ld /tmp" to see what permissions are set?  It should
be set to 777 (aka drwxrwxrwt).  

I know this doesn't help you but on my system the file cache module was
able to create that directory.

In the interim, you can probably set the "disable_cache" option in the
config file to 1 and this will bypass the cache (but leave you without
the speedy goodness).

Ben


On Wed, 2008-08-13 at 09:23 +0800, Lee Amy wrote:
> Hello,
> 
> I delete the contents of /tmp directory this morning, then when I use
> CMAP to show maps, it says following messages:
> 
> mkdir FileCache: Permission denied
> at /usr/lib/perl5/site_perl/5.8.3/Cache/FileBackend.pm line 222 
> 
> But I can "mkdir" under /tmp directory.
> 
> Could you tell me some tips?
> 
> Thank you very much~
> 
> Best Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
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Re: [gmod-cmap] Representation of Physical Map assignments?

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

Hi John,

I don't know if this is the most elegant solution but for markers and
such that are only assigned to a chromosome, I might create them as
features that span the full length of the chromosome.

Then, you can either use a spanning glyph like "span" or "i_beam" to
show the size. Or you can reduce the clutter by using a smaller glyph
like "right_facing_arrow" which will simply be placed in the middle of
feature.

The advantage of making a giant feature is that it will always be
displayed even when you are zoomed in.

Additionally, you could create separate feature types for those markers
to further differentiate them from the others.  (You will also want to
add them to the "add_name_correspondence" option in the config file.)

Hopefully this helps.  Sorry about the delay.  Let me know if you have
any other questions.

Ben

On Fri, 2008-08-08 at 12:10 +1200, John McCallum wrote:
> Hi
> I am interested in any suggestions or pointers to elegant implemented
> solutions in peoples CMAPs for the following:
> 
> In Allium we are at a rather primitive stage in proceedings and we have
> many markers and phenotypes that have been assigned to physical
> chromosomes using alien addition lines but not mapped. In  a number of
> cases we have markers mapped in one species but only chromosomally
> assigned in another and vice versa.
> These are quite important to us and I would like to represent these
> somehow so that in addition to viewing a linkage group one  could see
> markers assigned to the corresponding chromosome.
> 
> Any suggestions?
> 
> Regards
> John
> 
> Dr. John A. McCallum
> Crop & Food Research
> Private Bag 4704
> Christchurch
> New Zealand
> Work Ph 64 3 325 6400
> Home 64 3 328 7420
> Mobile 027 443 9033
> Fax 64 3 325 2074
> Email MCC...@CR...
> 
> 
> Visit our website at http://www.crop.cri.nz 
> ______________________________________________________
> CAUTION: The information contained in this email is privileged 
> and confidential.  If you read this message and you are not the 
> intended recipient, you are hereby notified that any use, 
> dissemination, distribution or reproduction of all or part of the 
> contents is prohibited. If you receive this message in error, 
> please notify the sender immediately.
> 
> Any opinions or views expressed in this message are those of the 
> individual sender and may not represent those of their employer.
> 
> 
> -------------------------------------------------------------------------
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[gmod-cmap] Help: Permission Problem

[Lee A. <ope...@gm...>]

Hello,

I delete the contents of /tmp directory this morning, then when I use CMAP
to show maps, it says following messages:

mkdir FileCache: Permission denied at
/usr/lib/perl5/site_perl/5.8.3/Cache/FileBackend.pm line 222

But I can "mkdir" under /tmp directory.

Could you tell me some tips?

Thank you very much~

Best Regards,

Amy Lee

[gmod-cmap] Representation of Physical Map assignments?

[John M. <McC...@cr...>]

Hi
I am interested in any suggestions or pointers to elegant implemented
solutions in peoples CMAPs for the following:

In Allium we are at a rather primitive stage in proceedings and we have
many markers and phenotypes that have been assigned to physical
chromosomes using alien addition lines but not mapped. In  a number of
cases we have markers mapped in one species but only chromosomally
assigned in another and vice versa.
These are quite important to us and I would like to represent these
somehow so that in addition to viewing a linkage group one  could see
markers assigned to the corresponding chromosome.

Any suggestions?

Regards
John

Dr. John A. McCallum
Crop & Food Research
Private Bag 4704
Christchurch
New Zealand
Work Ph 64 3 325 6400
Home 64 3 328 7420
Mobile 027 443 9033
Fax 64 3 325 2074
Email MCC...@CR...


Visit our website at http://www.crop.cri.nz 
______________________________________________________
CAUTION: The information contained in this email is privileged 
and confidential.  If you read this message and you are not the 
intended recipient, you are hereby notified that any use, 
dissemination, distribution or reproduction of all or part of the 
contents is prohibited. If you receive this message in error, 
please notify the sender immediately.

Any opinions or views expressed in this message are those of the 
individual sender and may not represent those of their employer.

Re: [gmod-cmap] Help: Cannot import data

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

Hi, 

This is a strange issue.  If there is an issue with the file, it should
be caught and reported by the validator (that runs before importation). 

The input file that you sent seems to work fine on my system, so the
issue is probably not that.  How are you importing the data
specifically?

You might want to try importing from the command line like this to see
if you get the same error (Note that this is the command line version of
what you probably already tried using the cmap_admin.pl menu system):

 $ bin/cmap_admin.pl -d DATASOURCE --action import_tab_data --map_set_acc MAP_SET_ACC /home/faga/dl/aa.dat

Replace DATASOURCE with the Data source name that you want to use and
the MAP_SET_ACC with the map set accession that you want to import the
maps into.

On another note, I've written and attached a quick, little, test script
that will be a little easier to run if there is some sort of issue with
the CPAN modules that it uses.  It doesn't touch the CMap db at all,
just reads the file and spits out a little report.  I expect it to have
the same error that you got previously.

Here is the output from when I ran it on your data file.

[faga@localhost bin]$ ./test_record_parser.pl /home/faga/dl/aa.dat 
Reading File.
field_compute
bind_header
Columns:
$VAR1 = 'map_acc';
$VAR2 = 'map_name';
$VAR3 = 'map_start';
$VAR4 = 'map_stop';
$VAR5 = 'feature_acc';
$VAR6 = 'feature_name';
$VAR7 = 'feature_aliases';
$VAR8 = 'feature_start';
$VAR9 = 'feature_stop';
$VAR10 = 'feature_type_acc';
$VAR11 = 'is_landmark';

    map_acc
    map_name
    map_start
    map_stop
    feature_acc
    feature_name
    feature_aliases
    feature_start
    feature_stop
    feature_type_acc
    is_landmark
151 rows of data in this document

Let me know how this all goes.  We should be able to get this figured
out.

Ben

On Tue, 2008-08-05 at 14:33 +0800, Lee Amy wrote:
> Hello,
> 
> I've installed the CMAP correctly and run demo database well. However,
> I encountered some problems while I'm going to import a QTL
> tab-delimited file. And I download the data file from the Gramene
> (following the attachment), and when I import this by using
> cmap_admin.pl it shows following error messages:
> 
> Error reading line number 1:
> map_acc map_name        map_start       map_stop        feature_acc
> feature_name    feature_aliases feature_start   feature_stop
> feature_type_acc        is_landmark
> at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/CMap/Admin/Import.pm line
> 890
> 
> Anyway, there's another problem I feel a little confused. The "Map
> Type" I see is still "Sequence" but return to Gramene I see there are
> several map types for CMAP. And the trifle is I cannot change the map
> type by my own. I don't know how to change it and I don't know whether
> it would be okay what if I change it from "QTL" map type.
> 
> Thank you very much~
> 
> Best Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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Re: [gmod-cmap] Help: QTL Demo

[Ken Youens-C. <kc...@cs...>]

The QTLs at Gramene are features like any other.  Their start and stop  
positions are linked to their associated markers, as I understand.  We  
also project their positions onto our sequence map via their  
associated markers's sequence positions.

ky

On Jul 28, 2008, at 3:50 PM, Ben Faga wrote:

> I'm  certainly not an expert on this but there is QTL data at gramene.
>
> Here is an example search:
>
> http://www.gramene.org/db/qtl/qtl_display?query=VGTM&search_field=&species=&x=0&y=0
>
> The "Position" link goes to CMap.
>
> Ben
>
> On Mon, 2008-07-28 at 22:21 +0800, Lee Amy wrote:
>> Hello,
>>
>> I'm a newbie in CMap and my group need do some work with CMap to show
>> their QTL information. Anyway, I don't know how to do that because I
>> know nothing about QTL format. I'm only a system administrator.
>>
>> So can anyone provide me some QTL full-detailed data and examples?
>> Then I can understand more about my task.
>>
>> Thank you very much~
>>
>> Best Regards,
>>
>> Amy Lee
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's  
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win  
>> great prizes
>> Grand prize is a trip for two to an Open Source event anywhere in  
>> the world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________ gmod-cmap mailing  
>> list gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-cmap
>
>
> -------------------------------------------------------------------------
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> challenge
> Build the coolest Linux based applications with Moblin SDK & win  
> great prizes
> Grand prize is a trip for two to an Open Source event anywhere in  
> the world
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> gmod-cmap mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-cmap

Re: [gmod-cmap] Help: QTL Demo

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

I'm  certainly not an expert on this but there is QTL data at gramene.  

Here is an example search:

http://www.gramene.org/db/qtl/qtl_display?query=VGTM&search_field=&species=&x=0&y=0

The "Position" link goes to CMap.

Ben

On Mon, 2008-07-28 at 22:21 +0800, Lee Amy wrote:
> Hello,
> 
> I'm a newbie in CMap and my group need do some work with CMap to show
> their QTL information. Anyway, I don't know how to do that because I
> know nothing about QTL format. I'm only a system administrator.
> 
> So can anyone provide me some QTL full-detailed data and examples?
> Then I can understand more about my task.
> 
> Thank you very much~
> 
> Best Regards,
> 
> Amy Lee
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________ gmod-cmap mailing list gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-cmap

[gmod-cmap] Help: QTL Demo

[Lee A. <ope...@gm...>]

Hello,

I'm a newbie in CMap and my group need do some work with CMap to show their
QTL information. Anyway, I don't know how to do that because I know nothing
about QTL format. I'm only a system administrator.

So can anyone provide me some QTL full-detailed data and examples? Then I
can understand more about my task.

Thank you very much~

Best Regards,

Amy Lee

Re: [gmod-cmap] Odd CMap Behavior

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

Hi Rex,

This is a little bit concerning.  I really want to figure this out.

My first thought (after "OMG, is there huge bug in CMap?!?") is that you
might be uploading map and feature types that are not defined in the
config file.  However, that sort of problem should have been caught
before the import happened.  I'm not very confident in that diagnosis.

Just to be sure I know what is happening, I want to restate the problem:

You have two installations of CMap (same machine?).  You have "old" data
files and "new" data files.  

Do the "old" data files import correctly?  (What I'm trying to figure
out is if the issue is between the data files or between versions of
CMap (AKA a new bug).

If it's not too much trouble, can you send (in another email, off-list)
examples of the import files and the config file (w/ username and
password removed)?

Hopefully, we can work this out.

Ben

On Wed, 2008-07-16 at 16:04 -0500, Rex Nelson wrote:
> Dear list:
> 
> We have a couple of CMap installations (V0.16 and V1.0).  We have had 
> a stable and predictable behavior from them both using "old" data 
> files.  We made "new" map sets for "new" map data and loaded the map 
> sets using each version's cmap_admin.pl script.  The loading went 
> without complaint but the resulting maps are a puzzle.  Some markers 
> that should show up in common between two maps don't, but some 
> reproducibly do show up.  The list of maps in the "add maps" list 
> seem to change between different runs of "make name-based 
> correspondences" using the cmap_admin.pl script on the same map sets. 
> I have looked in-depth at the "old" and "new" files and can SEE no 
> differences.  We have performed a "diff" of the old and new files 
> using BBEdit and it does not report any differences that we did not 
> expect.
> 
> Has anyone on the list seen such behavior before?
> 
> Rex

[gmod-cmap] Odd CMap Behavior

[Rex N. <nel...@ia...>]

Dear list:

We have a couple of CMap installations (V0.16 and V1.0).  We have had 
a stable and predictable behavior from them both using "old" data 
files.  We made "new" map sets for "new" map data and loaded the map 
sets using each version's cmap_admin.pl script.  The loading went 
without complaint but the resulting maps are a puzzle.  Some markers 
that should show up in common between two maps don't, but some 
reproducibly do show up.  The list of maps in the "add maps" list 
seem to change between different runs of "make name-based 
correspondences" using the cmap_admin.pl script on the same map sets. 
I have looked in-depth at the "old" and "new" files and can SEE no 
differences.  We have performed a "diff" of the old and new files 
using BBEdit and it does not report any differences that we did not 
expect.

Has anyone on the list seen such behavior before?

Rex
-- 
Rex Nelson Ph.D.
Ames,IA
nel...@ia...
(515) 294-1297
~~~_/) ~~~

Re: [gmod-cmap] Help: Table format

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

Hi Amy (and Ken if you see this),

You can import data in a couple ways.  

1. GFF3 Files
2. CMap Formated files and Hand insertion

You can read more about this in the "CREATING AND IMPORTING DATA"
section of the ADMINISTRATION document (perldoc
docs/ADMINISTRATION.pod).

1: GFF3 Files

The GFF3 spec allows you to create all the data in CMap in a single
file.

To use the GFF3 files, you need to have an up-to-date development
version of bioperl-live.  You can get the latest version at :
http://www.bioperl.org/wiki/Using_Subversion .

An example of a GFF3 file is located in the CMap distribution,
"data/test_data.gff".

2. Cmap Formatted Files

CMap also can take a tab delimited file format (perldoc
Bio::GMOD::CMap::Admin::Import).  However, each CMap formatted file is
only for maps in a single map set.  You will need to create species and
a map set using cmap_admin.pl first.  

Finally, as for the QTL data examples, I'm not sure.  Maybe Ken (who is
at Gramene) might have some example data for you.  If he can point me to
some data, I can create the GFF3 files for you.

Ben  


On Fri, 2008-07-11 at 14:24 +0800, Lee Amy wrote:
> Hello,
> 
> I've installed the CMAP 1.01 properly. And I'm only a user just know
> some skills so I don't know how to import my own data. Though I've
> read the administration document, I cannot grasp the main idea to do
> that. My most data is QTL maker table and I hope CMAP can read them
> correctly from MySQL
> 
> Anyway, what's the file format could I use? Furthermore, could I
> download some other QTL maker examples file to have a test? Or you can
> tell me more details step by step.
> 
> Thank you very much~
> 
> Best Regards,
> 
> Amy Lee
> 
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[gmod-cmap] Help: Table format

[Lee A. <ope...@gm...>]

Hello,

I've installed the CMAP 1.01 properly. And I'm only a user just know some
skills so I don't know how to import my own data. Though I've read the
administration document, I cannot grasp the main idea to do that. My most
data is QTL maker table and I hope CMAP can read them correctly from MySQL.

Anyway, what's the file format could I use? Furthermore, could I download
some other QTL maker examples file to have a test? Or you can tell me more
details step by step.

Thank you very much~

Best Regards,

Amy Lee

Re: [gmod-cmap] map height problem

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

Sorry, I don't think it is possible to turn off that feature.

Ben

On Wed, 2008-07-09 at 20:21 +0200, Charles Imbusch wrote:
> Hello Ken,
> 
> thanks for the information. Just being curious: is it possible to turn off
> this feature? :-)
> 
> cheers,
>   Charles
> 
> Ken Youens-Clark wrote:
> > That's a feature, not a bug.  CMap is horizontally centering the 
> > regions of correspondence so as to minimize slanting/crossing lines 
> > showing the correspondences.
> >
> > ky
> 
> 
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Re: [gmod-cmap] Help: Cannot import demo data

[Charles I. <ch...@im...>]

Hello Amy

[...]
> I use command by using ' mysql EXAMPLE_CMAP < tabtest-dump.sql' and 
> the example configuration defined the database EXAMPLE_CMAP.
>
> So what I puzzled is whether I should create a new database with the 
> corresponding tables. However, I found that the INSTALL.pod provides a 
> simple command to import demo database without creating database. 
> (Maybe I got wrong :( )
Yes, you have to create the database and the corresponding tables. For 
this purpose there already exist sql files in the cmap directory "sql". 
So the file you are looking for is "sql/cmap.create.mysql".

cheers,
  Charles

Re: [gmod-cmap] map height problem

[Charles I. <ch...@im...>]

Hello Ken,

thanks for the information. Just being curious: is it possible to turn off
this feature? :-)

cheers,
  Charles

Ken Youens-Clark wrote:
> That's a feature, not a bug.  CMap is horizontally centering the 
> regions of correspondence so as to minimize slanting/crossing lines 
> showing the correspondences.
>
> ky

[gmod-cmap] Help: Cannot import demo data

[Lee A. <ope...@gm...>]

Hello folks,

I'm a newbie in CMAP, anyway I've got some problems about import database.
The version of CMAP is 0.16 and Apache is 1.3.41, the database which I used
is MySQL 5.0.51a-community. I'm sure that I've installed the whole required
Perl modules.

While I'm trying to import the demo dump sql file tabtest-dump.sql from the
CMAP installation directory 'data', the error occurs with following words,

ERROR 1146 (42S02) at line 22: Table
'EXAMPLE_CMAP.cmap_correspondence_evidence' doesn't exist

I use command by using ' mysql EXAMPLE_CMAP < tabtest-dump.sql' and the
example configuration defined the database EXAMPLE_CMAP.

So what I puzzled is whether I should create a new database with the
corresponding tables. However, I found that the INSTALL.pod provides a
simple command to import demo database without creating database. (Maybe I
got wrong :( )

If I have to make one, could you tell me how to do that?

Thank you very much~

Regards,

Amy Lee

Re: [gmod-cmap] map height problem

[Ken Youens-C. <ky...@gm...>]

On Jul 5, 2008, at 5:19 AM, Charles Imbusch wrote:

> Hello,
>
> I'm a bioinformatics student (Jena, Germany) trying to get familiar  
> with
> cmap
> for a project. cmap is running and drawing beautiful maps. But there  
> is
> one problem I couldn't fix. When I make a comparison between a
> genetic and a sequence map, cmap draws one higher than the other.
> I uploaded a picture here:
> http://charles.imbusch.net/tmp/usysfd1V3.png
>
> What I would like to see is that "Chr. 01" have the same height as  
> well
> as the rest of the map. How can I do that?
>
> cheers,
> Charles

Charles,

That's a feature, not a bug.  CMap is horizontally centering the  
regions of correspondence so as to minimize slanting/crossing lines  
showing the correspondences.

ky

[gmod-cmap] map height problem

[Charles I. <ch...@im...>]

Hello,

I'm a bioinformatics student (Jena, Germany) trying to get familiar with 
cmap
for a project. cmap is running and drawing beautiful maps. But there is
one problem I couldn't fix. When I make a comparison between a
genetic and a sequence map, cmap draws one higher than the other.
I uploaded a picture here:
http://charles.imbusch.net/tmp/usysfd1V3.png

What I would like to see is that "Chr. 01" have the same height as well
as the rest of the map. How can I do that?

cheers,
Charles

[gmod-cmap] CMap 1.01 Released

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

Hi everyone,

Version 1.01 of CMap has been released.  

I'm quite excited about using GFF3 for data import/export which is
possible with this release.

You can get the new version from SourceForge,
http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129

Highlights of this release are:
 - Added a GFF3 parser and producer for easier and more complete data
   import and export (requires latest version of bioperl-live to import
   GFF).  
 - Added a module to serve data to CMap3D, a 3D viewer being developed
   by Chris Duran and Dave Edwards.

If you have any questions, please let me know.  

This is only an incremental update. For anyone who installed version
1.0, simply download the new release and run "perl Build.PL; ./Build;
sudo ./Build install".  No updates to the database or config files are
needed.

If you are updating from an older version, see the documentation in the
upgrade/ directory included in the package.

Full change list below.

Ben

1.01

- Modified the insert_feature_correspondence() method to allow
  correspondences between relational maps (this was done for speed).
  The check to make sure that no correspondences are made between
  relational maps has been moved to MakeCorrespondences.pm.
- Significantly, increased the speed of inserting features by removing
  the numeric check on the feature_stop value.
- Added a Bio::DB::SeqFeature::Store adaptor to allow GFF3 to be
  imported into CMap.  This GFF3 has extra pragma to define objects such
  as species and map sets.
- Added a module to output CMap style GFF3.
- For developers: To allow getting feature ids for features inserted in
  bulk, added a flag to the Generic.pm method insert_feature() to return
  an index into an array that is then returned when features are
  inserted.
- Added a module to serve data to CMap3D, a 3D viewer being developed by
  Chris Duran and Dave Edwards.