epaule/nameserver2

nameserver version 2

nameserver2's Issues

Gene NS : Find a gene (autocomplete)

Auto-complete is a bit funky.

I enter WBGene and it comes up with some suggestions based on what GeneIDs I've been using in this session, but underneath has some suggestions from the NS (or something).

When I pick one of the ones I've been using in the session it actually uses the NS suggested ID which I think is underneath.

Demo might be useful I think...

Gene: Merge genes

Is it good that you can merge a dead gene into another live gene

or worse a live gene with a cgc name into another gene

actually this causes a server error but the action appears to complete??

check out WBGene00230008 merge into WBGene00001217

Dump Features

enable dump features for Juancarlos

Gene: New Gene

cgc named genes work and check for existing
sequence named genes fail (New gene with name AH6.56 not created (Unable to open clonelist))

cannot perform the same task consecutively, e.g. merges/change of class

If you merge a gene, get the results page confirming the merge, you are not able to click on the 'merge genes' link on the task menu to merge another pair of genes. I have seen the same behaviour with 'change class'. You have to choose another task and then ask again for what you wanted in the first place.
I hope that makes sense :)
Ele

Gene NS: Add name (Enter ID of gene)

You can enter either GeneID or sequence_name here, so I suggest name of field matches what is in current NS: WBGeneID or Sequence_name

Gene: Split gene

WormBase Name Server: Cannot split gene New gene with name AH6.115 not created (does not exist) (for any gene??)

Gene: Remove name

Internal Server Error (500)

comment box on var nameserver

Please add a comment area on the variation nameserver. I would like to leave information and or references for the variations I create to make it easier for the var curator.

scripts

The following scripts use the gene NS in some way.

batch_addname.pl
batch_delname.pl
batch_kill.pl
batch_merge.pl
id_resurrect.pl
changegene.pl

ID consistency with each function

Low priority, but I have noticed some functions will accept either the Sequence_name or the WBGene ID and do the appropriate action, others will only accept the WBGene ID.

It might be good to be able to either only deal with WBGene ID or extend so that all functions can take either ID type?

P

add variation is broken

Option to ressurect a gene

This was previously omitted to retain control of the LIVE/DEAD status of genes in the database, but this is less of an issue these days.

Low priority, but would be useful.

P

Gene: Change class

gene sequence name is mandatory could we not use either the primary ID or a secondary sequence ID?

seq ID regex test for all functions

As just discussed........When a curator specifies the wrong species compared to the sequence name, could a check be made on the seqID regex in the Species.pm so that the output is correct :)

Thanks

Paul

Gene: Kill gene

Internal Server Error (500)

Gene: Change class

Internal Server Error (500)

Gene NS: Add name

Default "Name type to be added" in existing NS is CGC (not Sequence).
I think this was agreed with sequence curators because the add CGC name option is used more frequently than add Sequence.

-species flag set and change_class option

Can we make sure that species is output for every action that generates a email

class change doesn't, could the code also make an attempt at adding the correct code

CP = Coding -> Pseudogene
PC = Pseudogene -> Coding

It is a fair guess that it is one of these combinations going to be used.

P

naming of options

I'd like to suggest different names for the different options, to make
it very clear to users that they are working with IDs.

Email output expected from NS2

If the formatting could be preserved, that would be good as the following are used by scripts to process the request into geneace.

Merge Gene:

GENE MERGE
USER : pad - WBPerson1983
LIVE:retained geneID for Y35H6.3 - WBGene00021342
DEAD: killed geneID VY35H6BL.1 - WBGene00012160

New gene:

newgene.pl -seq CE7X_3.4 -who 1983 -load -id WBGene00235377 -species elegans -species elegans

Kill:

WBGene00021240
Remark "[pad] Converted this Gene into a Transposon_CDS/Pseudogene as it appears to be part of a transposable element."
WBPerson1983// pad

Split Gene:

splitgene.pl -old WBGene00021178 -new Y9C9A.112 -who 4025 -id WBGene00235376 -load -species elegans

Change Class:

changegene.pl -seq CE7X_3.2 -who 1983 -load -class

would be good if it could include the 2 letter code CP (Pseudogene to CDS) etc. etc.

---

I might have missed one, but hopefully not??

P

Gene: Remove Name

Might be good if the secondary ID being removed is actually connected to the gene??

1 import WBPerson1971 Tue, 30 Nov -001 00:01 CGC - -
1 addName wormpub Tue, 12 Sep 2006 17:50 CGC cha-1 -
2 changeName pad Thu, 03 Oct 2013 13:24 CGC unc-67 -
3 changeName pad Thu, 03 Oct 2013 13:24 Public_name unc-67 -
4 delName pad Thu, 03 Oct 2013 13:25 CGC unc-57 -
5 delName pad Thu, 03 Oct 2013 13:25 CGC unc-67

4. was never a valid secondary ID??

show last variation id

secondary names are case-insensitive

which means you can swap the case.

Probably can just change the chartype on the table and be fine, but needs testing.

Standardise the email output for all functions

This should be a low priority ticket, as script changes will be necessary if touched.

but it is irritating to have so much white space and different "token" names - "Command line" "command_line" etc. in the nameserver emails that get sent out.

@Paul-Davis

Change class 2

Could we change the Change class option drop down to be Transcript and not non-coding Transcript

Cheers

Change class Transposon

Could this also kill the gene in the NS as these get suppressed in geneace leaving a conflict when running the checking script.

It can be handled like any other http://www.sanger.ac.uk/sanger/Worm_NameServer_Gene/kill process.

Cheers

Paul

Error when adding new gene

Adding Cbn-wdr-5.1 to brenneri (WBGene00163257) and I get

Internal Server Error (500)
Your request for "/sanger/Worm_NameServer_Gene/add_name" failed. The reason is:

Unfortunately while trying to send you the contents that you requested, the server has hit a problem and cannot return what you have asked for.

Multiple gene mergers

Could a check be put in to prevent multiple merges or the same pair of genes

Please ;)

Event 1 03/03/2014 5:02PM
EMAIL : [email protected]
NAME : Eleanor Stanley
DEAD : killed geneid for OVOC12474 - WBGene00249283
LIVE : retained geneid for OVOC12476 - WBGene00249285
USER : es9 - WBPerson2062

Event 2 04/03/2014 8:29AM
EMAIL : [email protected]
NAME : Eleanor Stanley
DEAD : killed geneid for - WBGene00249283
LIVE : retained geneid for OVOC12476 - WBGene00249285
USER : es9 - WBPerson2062
WARNING : Merged gene WBGene00249283 was dead

gene cgc name

Add gene name does not have CGC option under "Name type to be added".

Gene NS: Find a gene (Public name of gene)

"Public name of gene" should be renamed "Name to add". It is not just Public_names we add through this page.

New gene option to include type dropdown.

Could we have the following dropdown as a manditory field when requesting a new gene

Type: CDS, Pseudogene, Transposon, Transcript

and this adds -bio and the specified type to the commandline.

Thanks

Paul

Gene NS : Find a gene

Can we have a "clear" option so we can run another query or do we need to press "find gene" again to run a new query?

nb. This is a suggested improvement to existing functionality.

Gene tests

General issue, most options only accept WBGene IDs as the primary ID to query/ work with.

*Find Gene: Will only look up data based on WBGeneID not good :(

*Add Name - appears to fail for CGC and Sequence name :(

*Remove name - Internal Server Error (500)

*New Gene - cgc named genes work and check for existing
sequence named genes fail (New gene with name AH6.56 not created (Unable to open clonelist))

*Kill gene - Internal Server Error (500)

*Merge gene - Internal Server Error (500)

*Split gene - WormBase Name Server: Cannot split gene New gene with name AH6.115 not created (does not exist) (for any gene??)

*Change class - Internal Server Error (500)

*Dump all genes - Worked yay ;)

Haven't tried load file

P

Gene NS: Can't create O.Volvulus genes

WormBase Name Server: Cannot generate new ID

New gene with name OVOC12995 not created (Invalid type)

Gene: Merge gene

Internal Server Error (500)

remove the hyperlinks in the result pages

... so Mary Ann can copy and paste

Gene: Find Gene

Will only look up data based on WBGeneID not good :(

Gene: Add Name

Add name, if you try and add a cgc name that already exists connected to another gene you get a

Internal Server Error (500)

Gene: Add Name

• appears to fail for CGC and Sequence name :(

Split from ticket #5