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
> 
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