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From: Weichen W. <we...@se...> - 2005-10-04 14:46:59
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Hi, Is there a plugin to load sequence files in EMBL format? Thanks, Weichen |
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From: Steve F. <sfi...@pc...> - 2005-10-04 15:07:12
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GUS::Supported::Plugin::InsertSequenceFeatures use: % ga GUS::Supported::Plugin::InsertSequenceFeatures --help to find out more about it. steve Weichen Wu wrote: > Hi, > > Is there a plugin to load sequence files in EMBL format? > > Thanks, > Weichen > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Angel P. <an...@ma...> - 2005-10-04 16:37:37
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Steve Fischer wrote: > GUS::Supported::Plugin::InsertSequenceFeatures > > use: > % ga GUS::Supported::Plugin::InsertSequenceFeatures --help > > to find out more about it. > > steve > > Weichen Wu wrote: > >> Hi, >> >> Is there a plugin to load sequence files in EMBL format? >> >> Thanks, >> Weichen >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: >> Power Architecture Resource Center: Free content, downloads, >> discussions, >> and more. http://solutions.newsforge.com/ibmarch.tmpl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |
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From: Angel P. <an...@ma...> - 2005-10-04 16:39:00
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A little more detail, We are trying to load IPI protein data, which is in UniProt format, which looks like EMBL format. Will this plugin instert AAsequence and features? Thanks, Angel Steve Fischer wrote: > GUS::Supported::Plugin::InsertSequenceFeatures > > use: > % ga GUS::Supported::Plugin::InsertSequenceFeatures --help > > to find out more about it. > > steve > > Weichen Wu wrote: > >> Hi, >> >> Is there a plugin to load sequence files in EMBL format? >> >> Thanks, >> Weichen >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: >> Power Architecture Resource Center: Free content, downloads, >> discussions, >> and more. http://solutions.newsforge.com/ibmarch.tmpl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 |
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From: Steve F. <sfi...@pc...> - 2005-10-04 16:59:20
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right now it is NASequence specific. but... i don't think it would take much to upgrade it to handle AASequence. volunteers? (i can't do it any time soon) also, the main thing about this plugin is that the mapping from input features to gus features is 100% configurable. steve Angel Pizarro wrote: > A little more detail, We are trying to load IPI protein data, which is > in UniProt format, which looks like EMBL format. Will this plugin > instert AAsequence and features? > > Thanks, > Angel > > Steve Fischer wrote: > >> GUS::Supported::Plugin::InsertSequenceFeatures >> >> use: >> % ga GUS::Supported::Plugin::InsertSequenceFeatures --help >> >> to find out more about it. >> >> steve >> >> Weichen Wu wrote: >> >>> Hi, >>> >>> Is there a plugin to load sequence files in EMBL format? >>> >>> Thanks, >>> Weichen >>> >>> >>> ------------------------------------------------------- >>> This SF.Net email is sponsored by: >>> Power Architecture Resource Center: Free content, downloads, >>> discussions, >>> and more. http://solutions.newsforge.com/ibmarch.tmpl >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: >> Power Architecture Resource Center: Free content, downloads, >> discussions, >> and more. http://solutions.newsforge.com/ibmarch.tmpl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > |
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From: Weichen W. <we...@se...> - 2005-10-06 18:22:11
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Hi, Since the Source Repository is temporary unavailable and the BioperlFeatMapperSet plugin is not in https://svn.cbil.upenn.edu/gus/GusAppFramework/trunk/Supported/plugin/perl/, can I find it somewhere else? Thanks, Weichen |
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From: Weichen W. <we...@se...> - 2005-10-08 04:02:57
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Hi, To use InsertSequenceFeatures plugin, is the mapping file is required? There is a genebank2gus.xml. Is there a mapping file for EMBL format available? Thanks, Weichen |
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From: Steve F. <sfi...@pc...> - 2005-10-08 11:29:43
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yes, the mapping file is required. you can use the genbank2gus.xml file if your embl file uses features and qualifiers that conform to the genbank/embl/ddbj feature table (see http://www.ncbi.nlm.nih.gov/collab/FT/). but, you must understand that input often does not conform, or, places data into qualifiers in the wrong way. in this case, you will need to provide your own mapping file. here is a snip from the documentation from the plugin (i just improved the doc in latest plugin version): -------- Another way to generate a template mapping file is by using the command reportFeatureQualifiers. This command analyzes a set of input files, and reports the feature/qualifier structure found in them. It can output the report in simple text form, or in XML that is a template for the mapping file. -------- steve Weichen Wu wrote: > Hi, > > To use InsertSequenceFeatures plugin, is the mapping file is required? > There is a genebank2gus.xml. Is there a mapping file for EMBL format > available? > > Thanks, > Weichen > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Weichen W. <we...@se...> - 2005-10-20 00:40:25
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Where can I find more document about mapping file or reportFeatureQualifiers? I will create a mapping file. Thanks, Weichen ----- Original Message ----- From: "Steve Fischer" <sfi...@pc...> To: "Weichen Wu" <we...@se...> Cc: <gus...@li...> Sent: Saturday, October 08, 2005 7:29 AM Subject: Re: [GUSDEV] mapping file > yes, the mapping file is required. you can use the genbank2gus.xml file > if your embl file uses features and qualifiers that conform to the > genbank/embl/ddbj feature table (see > http://www.ncbi.nlm.nih.gov/collab/FT/). > but, you must understand that input often does not conform, or, places > data into qualifiers in the wrong way. > > in this case, you will need to provide your own mapping file. > > here is a snip from the documentation from the plugin (i just improved the > doc in latest plugin version): > > -------- > Another way to generate a template mapping file is by using the command > reportFeatureQualifiers. This command analyzes a set of input files, and > reports the feature/qualifier structure found in them. It can output the > report in simple text form, or in XML that is a template for the mapping > file. > -------- > > steve > > Weichen Wu wrote: > >> Hi, >> >> To use InsertSequenceFeatures plugin, is the mapping file is required? >> There is a genebank2gus.xml. Is there a mapping file for EMBL format >> available? >> >> Thanks, >> Weichen >> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: >> Power Architecture Resource Center: Free content, downloads, discussions, >> and more. http://solutions.newsforge.com/ibmarch.tmpl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > CenterStudy > 0000600 0077645 0077645 00100322707 10322742046 012406 0 > ustar wewu > 0000000 0000000 > From cets Tue May 3 15:23:11 2005 > Date: 03 May 2005 15:23:11 -0400 > From: Ask CETS <ce...@ho...> > Subject: DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA > Message-ID: <111...@ho...> > X-IMAP: 1101936235 0000000030 > Status: RO > > Dear Email User, > > Hello! My name is Paul Shaffer, and I'm a real person (not a computer > program). I'm the "clerk" for the Eniac computer system here at SEAS. > > In order to keep track of your email, the computer needs to keep some > special directory information (things like which messages you've read). > This info is kept in an email message, which is kept in your mailbox. In > fact, it is THIS VERY MESSAGE that keeps the directory info. > > Some other points you should know: > > + Don't delete this message - it will just come back if you do. > > + This message is created when you read mail using POP or IMAP, but > you only see it when you read mail without POP or IMAP (e.g mutt or elm). > > + This message is like a bookmark. POP or IMAP (the infrastructure that > lets Netscape mail and Eudora work) creates it when you stop reading > and looks for it when you start again. It is stored here (rather than > on your PC) so that you can use more than one machine and it will > always be available. > > So, sit back, relax, and just IGNORE this message. You need it. You > can't get rid of it, so you might as well just get used to it. If you > have any questions about what's going on, you can call 898-4707. > > Thank you for your understanding. > |
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From: Steve F. <sfi...@pc...> - 2005-10-20 02:21:01
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the only documentation is: ga GUS::Supported::Plugin::InsertSequenceFeatures --help plus, use the default mapping file, and the default special case handler (GUS::Supported::SpecialCaseQualifierHandler) ask questions as they come up. steve Weichen Wu wrote: > Where can I find more document about mapping file or > reportFeatureQualifiers? I will create a mapping file. > > Thanks, > Weichen > > ----- Original Message ----- From: "Steve Fischer" > <sfi...@pc...> > To: "Weichen Wu" <we...@se...> > Cc: <gus...@li...> > Sent: Saturday, October 08, 2005 7:29 AM > Subject: Re: [GUSDEV] mapping file > > >> yes, the mapping file is required. you can use the genbank2gus.xml >> file if your embl file uses features and qualifiers that conform to >> the genbank/embl/ddbj feature table (see >> http://www.ncbi.nlm.nih.gov/collab/FT/). >> but, you must understand that input often does not conform, or, >> places data into qualifiers in the wrong way. >> >> in this case, you will need to provide your own mapping file. >> >> here is a snip from the documentation from the plugin (i just >> improved the doc in latest plugin version): >> >> -------- >> Another way to generate a template mapping file is by using the >> command reportFeatureQualifiers. This command analyzes a set of >> input files, and reports the feature/qualifier structure found in >> them. It can output the report in simple text form, or in XML that >> is a template for the mapping file. >> -------- >> >> steve >> >> Weichen Wu wrote: >> >>> Hi, >>> >>> To use InsertSequenceFeatures plugin, is the mapping file is >>> required? There is a genebank2gus.xml. Is there a mapping file for >>> EMBL format available? >>> >>> Thanks, >>> Weichen >>> >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.Net email is sponsored by: >>> Power Architecture Resource Center: Free content, downloads, >>> discussions, >>> and more. http://solutions.newsforge.com/ibmarch.tmpl >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> CenterStudy 0000600 0077645 0077645 00100322707 10322742046 012406 0 >> ustar wewu 0000000 0000000 From cets Tue May 3 15:23:11 2005 >> Date: 03 May 2005 15:23:11 -0400 >> From: Ask CETS <ce...@ho...> >> Subject: DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA >> Message-ID: <111...@ho...> >> X-IMAP: 1101936235 0000000030 >> Status: RO >> >> Dear Email User, >> >> Hello! My name is Paul Shaffer, and I'm a real person (not a computer >> program). I'm the "clerk" for the Eniac computer system here at SEAS. >> >> In order to keep track of your email, the computer needs to keep some >> special directory information (things like which messages you've read). >> This info is kept in an email message, which is kept in your >> mailbox. In >> fact, it is THIS VERY MESSAGE that keeps the directory info. >> >> Some other points you should know: >> >> + Don't delete this message - it will just come back if you do. >> >> + This message is created when you read mail using POP or IMAP, but >> you only see it when you read mail without POP or IMAP (e.g mutt or >> elm). >> >> + This message is like a bookmark. POP or IMAP (the infrastructure that >> lets Netscape mail and Eudora work) creates it when you stop reading >> and looks for it when you start again. It is stored here (rather than >> on your PC) so that you can use more than one machine and it will >> always be available. >> >> So, sit back, relax, and just IGNORE this message. You need it. You >> can't get rid of it, so you might as well just get used to it. If you >> have any questions about what's going on, you can call 898-4707. >> >> Thank you for your understanding. >> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Weichen W. <we...@se...> - 2005-10-10 21:21:19
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My GUS 3.5 instance is complete new and I am loading NCBI Taxon data files
using LoadTaxon.pm plugin. I have this problem about null value of tax_id.
Do I need load anything else before loading taxon?
The log is as follows:
[wewu@noodle ncbi_taxon]$ ga GUS::Supported::Plugin::LoadTaxon --nodes
nodes.dmp --names names.dmp --gencode gencode.dmp --merged merged.dmp
Mon Oct 10 16:37:29 2005 ARGS algoinvo 1
<... skip some lines>
Mon Oct 10 16:37:29 2005 Doing merge and NCBI tax id '12' not in
database, skipping
<...skip many lines>
Mon Oct 10 16:37:33 2005 Doing merge and NCBI tax id '349635' not in
database, skipping
Mon Oct 10 16:37:33 2005 Updating and inserting SRes.GeneticCode
Mon Oct 10 16:37:50 2005 Number processed: 1000
<...skip many lines>
Mon Oct 10 16:54:33 2005 Number processed: 278000
Mon Oct 10 16:54:34 2005 Inserting and updating TaxonName
DBD::Pg::st execute failed: ERROR: null value in column "taxon_id" violates
not-null constraint
ERROR:
SQL ERROR!! involving
INSERT INTO SRes.TaxonName ( unique_name_variant, group_write,
other_read, group_read, name, taxon_id, user_read, row_user_id,
modification_date, name_class, other_write, row_alg_invocation_id,
row_project_id, taxon_name_id, row_group_id, user_write )
VALUES ( null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1 at
/home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166
Thanks,
Weichen
----- Original Message -----
From: "Steve Fischer" <sfi...@pc...>
To: "Weichen Wu" <we...@se...>
Cc: <gus...@li...>
Sent: Saturday, October 08, 2005 7:29 AM
Subject: Re: [GUSDEV] mapping file
> yes, the mapping file is required. you can use the genbank2gus.xml file
> if your embl file uses features and qualifiers that conform to the
> genbank/embl/ddbj feature table (see
> http://www.ncbi.nlm.nih.gov/collab/FT/).
> but, you must understand that input often does not conform, or, places
> data into qualifiers in the wrong way.
>
> in this case, you will need to provide your own mapping file.
>
> here is a snip from the documentation from the plugin (i just improved the
> doc in latest plugin version):
>
> --------
> Another way to generate a template mapping file is by using the command
> reportFeatureQualifiers. This command analyzes a set of input files, and
> reports the feature/qualifier structure found in them. It can output the
> report in simple text form, or in XML that is a template for the mapping
> file.
> --------
>
> steve
>
> Weichen Wu wrote:
>
>> Hi,
>>
>> To use InsertSequenceFeatures plugin, is the mapping file is required?
>> There is a genebank2gus.xml. Is there a mapping file for EMBL format
>> available?
>>
>> Thanks,
>> Weichen
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads, discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: <pi...@pc...> - 2005-10-11 13:04:58
|
Merges are updates to the existing db. It occurs when NCBI merges or
transforms
one tax_id with another and the merge file is cumulative. If this is the first
loading of the NCBI taxon, then your db instance will have none of
these tax id
to merge and you'll get this message. In the future you will get fewer.
Therefore, this is OK.
The failure you get is more serious. Did you provide the entire node.dmp file.
It looks like you didn't get the taxon table loaded. That must occur before
loading the taxonname table. One thought, I think you need to load with commit
on.
Deborah
Quoting Weichen Wu <we...@se...>:
> My GUS 3.5 instance is complete new and I am loading NCBI Taxon data
> files using LoadTaxon.pm plugin. I have this problem about null value
> of tax_id. Do I need load anything else before loading taxon?
> The log is as follows:
>
> [wewu@noodle ncbi_taxon]$ ga GUS::Supported::Plugin::LoadTaxon
> --nodes nodes.dmp --names names.dmp --gencode gencode.dmp --merged
> merged.dmp
> Mon Oct 10 16:37:29 2005 ARGS algoinvo 1
> <... skip some lines>
> Mon Oct 10 16:37:29 2005 Doing merge and NCBI tax id '12' not
> in database, skipping
> <...skip many lines>
> Mon Oct 10 16:37:33 2005 Doing merge and NCBI tax id '349635'
> not in database, skipping
> Mon Oct 10 16:37:33 2005 Updating and inserting SRes.GeneticCode
> Mon Oct 10 16:37:50 2005 Number processed: 1000
> <...skip many lines>
> Mon Oct 10 16:54:33 2005 Number processed: 278000
> Mon Oct 10 16:54:34 2005 Inserting and updating TaxonName
>
> DBD::Pg::st execute failed: ERROR: null value in column "taxon_id"
> violates not-null constraint
> ERROR:
> SQL ERROR!! involving
> INSERT INTO SRes.TaxonName ( unique_name_variant, group_write,
> other_read, group_read, name, taxon_id, user_read, row_user_id,
> modification_date, name_class, other_write, row_alg_invocation_id,
> row_project_id, taxon_name_id, row_group_id, user_write )
> VALUES ( null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1
> at /home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 166
>
> Thanks,
> Weichen
>
>
>
> ----- Original Message ----- From: "Steve Fischer" <sfi...@pc...>
> To: "Weichen Wu" <we...@se...>
> Cc: <gus...@li...>
> Sent: Saturday, October 08, 2005 7:29 AM
> Subject: Re: [GUSDEV] mapping file
>
>
>> yes, the mapping file is required. you can use the genbank2gus.xml
>> file if your embl file uses features and qualifiers that conform to
>> the genbank/embl/ddbj feature table (see
>> http://www.ncbi.nlm.nih.gov/collab/FT/).
>> but, you must understand that input often does not conform, or,
>> places data into qualifiers in the wrong way.
>>
>> in this case, you will need to provide your own mapping file.
>>
>> here is a snip from the documentation from the plugin (i just
>> improved the doc in latest plugin version):
>>
>> --------
>> Another way to generate a template mapping file is by using the
>> command reportFeatureQualifiers. This command analyzes a set of
>> input files, and reports the feature/qualifier structure found in
>> them. It can output the report in simple text form, or in XML that
>> is a template for the mapping file.
>> --------
>>
>> steve
>>
>> Weichen Wu wrote:
>>
>>> Hi,
>>>
>>> To use InsertSequenceFeatures plugin, is the mapping file is
>>> required? There is a genebank2gus.xml. Is there a mapping file for
>>> EMBL format available?
>>>
>>> Thanks,
>>> Weichen
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads, discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Michael S. <msa...@pc...> - 2005-10-11 13:15:07
|
I knew this sounded familiar-- Debbie's post refreshed my memory. This is an open issue and there is an entry in the tracker for it: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=45 Based on the tracker comments, this error only appears when not in commit mode. I've increased the priority in the tracker, and this is scheduled for resolution in the next release. --Mike On 10/11/05 9:04 AM, "pi...@pc..." <pi...@pc...> wrote: > Merges are updates to the existing db. It occurs when NCBI merges or > transforms > one tax_id with another and the merge file is cumulative. If this is the first > loading of the NCBI taxon, then your db instance will have none of > these tax id > to merge and you'll get this message. In the future you will get fewer. > Therefore, this is OK. > > The failure you get is more serious. Did you provide the entire node.dmp file. > It looks like you didn't get the taxon table loaded. That must occur before > loading the taxonname table. One thought, I think you need to load with commit > on. > > Deborah > > > Quoting Weichen Wu <we...@se...>: > >> My GUS 3.5 instance is complete new and I am loading NCBI Taxon data >> files using LoadTaxon.pm plugin. I have this problem about null value >> of tax_id. Do I need load anything else before loading taxon? >> The log is as follows: >> >> [wewu@noodle ncbi_taxon]$ ga GUS::Supported::Plugin::LoadTaxon >> --nodes nodes.dmp --names names.dmp --gencode gencode.dmp --merged >> merged.dmp >> Mon Oct 10 16:37:29 2005 ARGS algoinvo 1 >> <... skip some lines> >> Mon Oct 10 16:37:29 2005 Doing merge and NCBI tax id '12' not >> in database, skipping >> <...skip many lines> >> Mon Oct 10 16:37:33 2005 Doing merge and NCBI tax id '349635' >> not in database, skipping >> Mon Oct 10 16:37:33 2005 Updating and inserting SRes.GeneticCode >> Mon Oct 10 16:37:50 2005 Number processed: 1000 >> <...skip many lines> >> Mon Oct 10 16:54:33 2005 Number processed: 278000 >> Mon Oct 10 16:54:34 2005 Inserting and updating TaxonName >> >> DBD::Pg::st execute failed: ERROR: null value in column "taxon_id" >> violates not-null constraint >> ERROR: >> SQL ERROR!! involving >> INSERT INTO SRes.TaxonName ( unique_name_variant, group_write, >> other_read, group_read, name, taxon_id, user_read, row_user_id, >> modification_date, name_class, other_write, row_alg_invocation_id, >> row_project_id, taxon_name_id, row_group_id, user_write ) >> VALUES ( null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? ) >> Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1 >> at /home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm >> line 166 >> >> Thanks, >> Weichen >> >> >> >> ----- Original Message ----- From: "Steve Fischer" <sfi...@pc...> >> To: "Weichen Wu" <we...@se...> >> Cc: <gus...@li...> >> Sent: Saturday, October 08, 2005 7:29 AM >> Subject: Re: [GUSDEV] mapping file >> >> >>> yes, the mapping file is required. you can use the genbank2gus.xml >>> file if your embl file uses features and qualifiers that conform to >>> the genbank/embl/ddbj feature table (see >>> http://www.ncbi.nlm.nih.gov/collab/FT/). >>> but, you must understand that input often does not conform, or, >>> places data into qualifiers in the wrong way. >>> >>> in this case, you will need to provide your own mapping file. >>> >>> here is a snip from the documentation from the plugin (i just >>> improved the doc in latest plugin version): >>> >>> -------- >>> Another way to generate a template mapping file is by using the >>> command reportFeatureQualifiers. This command analyzes a set of >>> input files, and reports the feature/qualifier structure found in >>> them. It can output the report in simple text form, or in XML that >>> is a template for the mapping file. >>> -------- >>> >>> steve >>> >>> Weichen Wu wrote: >>> >>>> Hi, >>>> >>>> To use InsertSequenceFeatures plugin, is the mapping file is >>>> required? There is a genebank2gus.xml. Is there a mapping file for >>>> EMBL format available? >>>> >>>> Thanks, >>>> Weichen >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------- >>>> This SF.Net email is sponsored by: >>>> Power Architecture Resource Center: Free content, downloads, discussions, >>>> and more. http://solutions.newsforge.com/ibmarch.tmpl >>>> _______________________________________________ >>>> Gusdev-gusdev mailing list >>>> Gus...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: >> Power Architecture Resource Center: Free content, downloads, discussions, >> and more. http://solutions.newsforge.com/ibmarch.tmpl >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: > Power Architecture Resource Center: Free content, downloads, discussions, > and more. http://solutions.newsforge.com/ibmarch.tmpl > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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