[Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

classic Classic list List threaded Threaded
7 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Abraham Darius Llave IRRI
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Stephen Ficklin-2
Hi Darius,

What version of Tripal are you using?  I think we can easily add a box on the KEGG loader page that lets you specify the organism and provide a fix for you.

Stephen


On 7/21/2014 4:32 AM, Abraham Darius Llave (IRRI) wrote:
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Abraham Darius Llave IRRI
Oh, forgetful me, while typing the email I keep on telling myself I should not forget the version... Hehehe.

It's 6.x-1.1 .


On Tue, Jul 22, 2014 at 3:49 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Darius,

What version of Tripal are you using?  I think we can easily add a box on the KEGG loader page that lets you specify the organism and provide a fix for you.

Stephen



On 7/21/2014 4:32 AM, Abraham Darius Llave (IRRI) wrote:
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Stephen Ficklin-2
Hi Abraham,

I have submitted a fix to the development branch (6.x-1.x) for Tripal v1.1 KEGG module.  If you pull that branch and update the database you should now be able to specify an organism when importing KEGG results.   Can you test and make sure it works fine for you?

To update the code and apply database updates:
cd [kegg analysis module dir]
git checkout 6.x-1.x
git pull
drush updatedb

Stephen

On 7/21/2014 9:31 PM, Abraham Darius Llave (IRRI) wrote:
Oh, forgetful me, while typing the email I keep on telling myself I should not forget the version... Hehehe.

It's 6.x-1.1 .


On Tue, Jul 22, 2014 at 3:49 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Darius,

What version of Tripal are you using?  I think we can easily add a box on the KEGG loader page that lets you specify the organism and provide a fix for you.

Stephen



On 7/21/2014 4:32 AM, Abraham Darius Llave (IRRI) wrote:
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




.

The International Rice Research Institute is a member of the CGIAR consortium


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Abraham Darius Llave IRRI
Hello Stephen.

I have performed as above and yes, I can now specify to which organism should the KEGG data be matched.
I re-ran the job and it was completed half an hour ago. 
Though the "KEGG Analysis Reports" of the Resources sidebar now displays relevant information as can be seen below,

-----------------------------
Inline image 1
-------

... however, I still got some warning and error messages upon running the job. Do you think we need to have some other actions to be sure that the KEGG data were loaded correctly?  I attached the log file of drush output for you to examine. 

 


On Thu, Jul 24, 2014 at 4:51 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Abraham,

I have submitted a fix to the development branch (6.x-1.x) for Tripal v1.1 KEGG module.  If you pull that branch and update the database you should now be able to specify an organism when importing KEGG results.   Can you test and make sure it works fine for you?

To update the code and apply database updates:
cd [kegg analysis module dir]
git checkout 6.x-1.x
git pull
drush updatedb

Stephen


On 7/21/2014 9:31 PM, Abraham Darius Llave (IRRI) wrote:
Oh, forgetful me, while typing the email I keep on telling myself I should not forget the version... Hehehe.

It's 6.x-1.1 .


On Tue, Jul 22, 2014 at 3:49 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Darius,

What version of Tripal are you using?  I think we can easily add a box on the KEGG loader page that lets you specify the organism and provide a fix for you.

Stephen



On 7/21/2014 4:32 AM, Abraham Darius Llave (IRRI) wrote:
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




.

The International Rice Research Institute is a member of the CGIAR consortium




--

.


The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

20140724-1025_load-kegg-data-now-with-organism-selection-DONT-USE-UNIQUENAME.log (1M) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Stephen Ficklin-2
Hi Abraham,

Thanks for sending the log file.  It looks like the parser had some issues with the q00002.keg file.  Would you mind forwarding that along to me (privately if you like) and I can see what might be going awry?

Stephen

On 7/24/2014 1:38 AM, Abraham Darius Llave (IRRI) wrote:
Hello Stephen.

I have performed as above and yes, I can now specify to which organism should the KEGG data be matched.
I re-ran the job and it was completed half an hour ago. 
Though the "KEGG Analysis Reports" of the Resources sidebar now displays relevant information as can be seen below,

-----------------------------
Inline image 1
-------

... however, I still got some warning and error messages upon running the job. Do you think we need to have some other actions to be sure that the KEGG data were loaded correctly?  I attached the log file of drush output for you to examine. 

 


On Thu, Jul 24, 2014 at 4:51 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Abraham,

I have submitted a fix to the development branch (6.x-1.x) for Tripal v1.1 KEGG module.  If you pull that branch and update the database you should now be able to specify an organism when importing KEGG results.   Can you test and make sure it works fine for you?

To update the code and apply database updates:
cd [kegg analysis module dir]
git checkout 6.x-1.x
git pull
drush updatedb

Stephen


On 7/21/2014 9:31 PM, Abraham Darius Llave (IRRI) wrote:
Oh, forgetful me, while typing the email I keep on telling myself I should not forget the version... Hehehe.

It's 6.x-1.1 .


On Tue, Jul 22, 2014 at 3:49 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Darius,

What version of Tripal are you using?  I think we can easily add a box on the KEGG loader page that lets you specify the organism and provide a fix for you.

Stephen



On 7/21/2014 4:32 AM, Abraham Darius Llave (IRRI) wrote:
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




.

The International Rice Research Institute is a member of the CGIAR consortium




--

.


The International Rice Research Institute is a member of the CGIAR consortium


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-tripal-devel] KEGG Annotation Data and Feature Name Shared Across Organisms

Abraham Darius Llave IRRI
Hello.

Since all of these are publicly available data, I'm just going to send all of those files in the TAR archive.


On Thu, Jul 24, 2014 at 11:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Abraham,

Thanks for sending the log file.  It looks like the parser had some issues with the q00002.keg file.  Would you mind forwarding that along to me (privately if you like) and I can see what might be going awry?

Stephen


On 7/24/2014 1:38 AM, Abraham Darius Llave (IRRI) wrote:
Hello Stephen.

I have performed as above and yes, I can now specify to which organism should the KEGG data be matched.
I re-ran the job and it was completed half an hour ago. 
Though the "KEGG Analysis Reports" of the Resources sidebar now displays relevant information as can be seen below,

-----------------------------
Inline image 1
-------

... however, I still got some warning and error messages upon running the job. Do you think we need to have some other actions to be sure that the KEGG data were loaded correctly?  I attached the log file of drush output for you to examine. 

 


On Thu, Jul 24, 2014 at 4:51 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Abraham,

I have submitted a fix to the development branch (6.x-1.x) for Tripal v1.1 KEGG module.  If you pull that branch and update the database you should now be able to specify an organism when importing KEGG results.   Can you test and make sure it works fine for you?

To update the code and apply database updates:
cd [kegg analysis module dir]
git checkout 6.x-1.x
git pull
drush updatedb

Stephen


On 7/21/2014 9:31 PM, Abraham Darius Llave (IRRI) wrote:
Oh, forgetful me, while typing the email I keep on telling myself I should not forget the version... Hehehe.

It's 6.x-1.1 .


On Tue, Jul 22, 2014 at 3:49 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Darius,

What version of Tripal are you using?  I think we can easily add a box on the KEGG loader page that lets you specify the organism and provide a fix for you.

Stephen



On 7/21/2014 4:32 AM, Abraham Darius Llave (IRRI) wrote:
Hello Tripal Devs! Can you be of assistance?

So formerly, I have loaded KAAS-annotated data for Sorghum bicolor version 1.4 transcripts. Eventually, our team decided to move to version 2.1 and have to repeat the process again. However, we also now have two closely-related Sorghum plants added into Chado (apart from S. bicolor), with their genome and features generated with the aid of Sorghum bicolor 2.1's.

The problem is, when I try to loaded the KEGG file, I get this error message:
 
xxx------------------------------------xxx
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G467000.1' matches   [error]
more than one feature and is being skipped.
WD tr_kegg_parse: Failed (Ambiguous): 'Sobic.001G281900.1' matches
more than one feature and is being skipped.
xxx------------------------------------xxx

Enabling the use of the unique name still does not let me through but with a different message now

xxx------------------------------------xxx
WD tr_kegg_parse: Failed: 'Sobic.004G037000.1' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.004G037000.1.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.2' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.2.
WD tr_kegg_parse: Failed: 'Sobic.003G012200.3' cannot find a matching[error]
feature in the databasef.  RE: ; LINE: Sobic.003G012200.3.
xxx------------------------------------xxx

For the first case, I presume it happens because in function 

tripal_analysis_kegg_check_line_handle_feature(..) 

in
  <wwwroot>/sites/all/modules/tripal_kegg_analysis/includes/parseKAASHeir.inc, 

a call to tripal_core_chado_select(..) does not include the organism ID as one of the filters.

xxx------------------------------------xxx
 $feature_arr = tripal_core_chado_select('feature', array('feature_id'), $select, $options);

    if (count($feature_arr) > 1) {
      watchdog('tr_kegg_parse', "Failed (Ambiguous): '%feature' matches more than one feature and is being skipped.",
        array('%feature' => $feature), 'error');
      return;
    }
xxx------------------------------------xxx

I tried including the organism ID in the filters, so I added
 
xxx------------------------------------xxx
$select['organism_id'] = 14;
xxx------------------------------------xxx

before the call to tripal_core_chado_select(..) , but I get messages like these now:

xxx------------------------------------xxx
WD tripal_core: Cannot find property ''.                             [error]
WD tripal_feature: tripal_feature_analysis_insert_property: Failed to[warning]
insert analysis feature property
WD tr_kegg_parse: Failed: Could not add orthlog to feature.  Feature [error]
Id: 6369275, Ortholog: ''
WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare: 'fk_feature_cvterm_cvterm_idnacv'     [error]
statement already prepared with different arguments! You want to
prepare 
PREPARE fk_feature_cvterm_cvterm_idnacv (int) AS SELECT cvterm_id
FROM {cvterm} WHERE name IS NULL AND cv_id = $1 
 with 
Array
(
    [0] => int
)

 and the existing statement is 
PREPARE fk_feature_cvterm_cvterm_idnacv (text, int) AS SELECT
cvterm_id FROM {cvterm} WHERE name = $1 AND cv_id = $2 
 with 
Array
(
    [0] => text
    [1] => int
)

WD tripal_core: chado_prepare:                                       [error]
'uqsel_feature_cvterm_feature_cvterm_c1' statement already prepared
with different arguments! You want to prepare 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int) AS
SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND pub_id = $2 AND rank = $3 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

 and the existing statement is 
PREPARE uqsel_feature_cvterm_feature_cvterm_c1 (int, int, int, int)
AS SELECT feature_id, cvterm_id, pub_id, rank FROM {feature_cvterm}
WHERE feature_id = $1 AND cvterm_id = $2 AND pub_id = $3 AND rank =
$4 
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
    [3] => int
)

WD tripal_core: chado_prepare: 'ins_featurecvterm_cvfepu' statement  [error]
already prepared with different arguments! You want to prepare 
PREPARE ins_featurecvterm_cvfepu (int, int) AS INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES ($1, $2)
 with 
Array
(
    [0] => int
    [1] => int
)

 and the existing statement is 
PREPARE ins_featurecvterm_cvfepu (int, int, int) AS INSERT INTO
{feature_cvterm} (cvterm_id, feature_id, pub_id) VALUES ($1, $2, $3)
 with 
Array
(
    [0] => int
    [1] => int
    [2] => int
)

WD tripal_core: tripal_core_chado_insert: not able to prepare        [error]
'ins_featurecvterm_cvfepu' statement for: INSERT INTO
{feature_cvterm} (feature_id, pub_id) VALUES (%d, %d)
WD tripal_feature: tripal_feature_add_cvterm: The feature cvterm     [warning]
entry for feature, 6369275, could not be added: .
xxx------------------------------------xxx

So, how do I get to load KEGG file if the feature name is shared within multiple organisms?


----

Abraham Darius S. Llave

Junior Specialist - Bioinformatics | C4 Rice Center

International Rice Research Institute

Los Baños, Laguna 4027

Republic of the  Philippines

[hidden email]
+63-49-536-2701 extension 2643

 



The International Rice Research Institute is a member of the CGIAR consortium

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds


_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




.

The International Rice Research Institute is a member of the CGIAR consortium




--

.


The International Rice Research Institute is a member of the CGIAR consortium




--
.

The International Rice Research Institute is a member of the CGIAR consortium
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel

sbicolor2.1-phytozome10_20140715-hier.tar.gz (868K) Download Attachment