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Question about loading CDS coordinates

青木康洋
Dear  Apollo team members,

I installed Apollo 2.0.4 and used "add_transcript_from_gff3_to_annotations.pl"
script to bulk load GFF3 file.
But some loaded CDS coordinates were different from original ones.
Maybe those were recalculated.
How can I load original CDS coordinates?

Thanks,
Yasuhiro




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Re: Question about loading CDS coordinates

nathandunn

By default it should do this since the default apollo variable ‘use_cds_for_new_transcripts’ is set to true.   However, we identified a bug:


We should have a fix for this relatively soon (and will repost once its merged).  

Thanks for bringing it to our attention and sorry for the inconvenience.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Oct 6, 2016, at 8:20 AM, 青木康洋 <[hidden email]> wrote:

Dear  Apollo team members,

I installed Apollo 2.0.4 and used "add_transcript_from_gff3_to_annotations.pl"
script to bulk load GFF3 file.
But some loaded CDS coordinates were different from original ones.
Maybe those were recalculated.
How can I load original CDS coordinates?

Thanks,
Yasuhiro



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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Re: Question about loading CDS coordinates

nathandunn

This is fixed and in master now (thanks Deepak!) if you want to re-clone or pull you should pick it up.   The default is what you want so no configuration changes will need to be made.    


Nathan

On Oct 6, 2016, at 9:50 AM, Nathan Dunn <[hidden email]> wrote:


By default it should do this since the default apollo variable ‘use_cds_for_new_transcripts’ is set to true.   However, we identified a bug:


We should have a fix for this relatively soon (and will repost once its merged).  

Thanks for bringing it to our attention and sorry for the inconvenience.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Oct 6, 2016, at 8:20 AM, 青木康洋 <[hidden email]> wrote:

Dear  Apollo team members,

I installed Apollo 2.0.4 and used "add_transcript_from_gff3_to_annotations.pl"
script to bulk load GFF3 file.
But some loaded CDS coordinates were different from original ones.
Maybe those were recalculated.
How can I load original CDS coordinates?

Thanks,
Yasuhiro



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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Re: Question about loading CDS coordinates

青木康洋
Thank you.
That helps me a lot.

Yasuhiro

2016-10-07 2:43 GMT+09:00 Nathan Dunn <[hidden email]>:

>
> This is fixed and in master now (thanks Deepak!) if you want to re-clone or
> pull you should pick it up.   The default is what you want so no
> configuration changes will need to be made.
>
>
> Nathan
>
> On Oct 6, 2016, at 9:50 AM, Nathan Dunn <[hidden email]> wrote:
>
>
> By default it should do this since the default apollo variable
> ‘use_cds_for_new_transcripts’ is set to true.   However, we identified a
> bug:
>
> https://github.com/GMOD/Apollo/issues/1297
>
> We should have a fix for this relatively soon (and will repost once its
> merged).
>
> Thanks for bringing it to our attention and sorry for the inconvenience.
>
> Nathan Dunn, PhD
> Berkeley Bioinformatics Open-source Projects (BBOP)
> Genomics Division, Lawrence Berkeley National Laboratory
> [hidden email]
>
>
> On Oct 6, 2016, at 8:20 AM, 青木康洋 <[hidden email]> wrote:
>
> Dear  Apollo team members,
>
> I installed Apollo 2.0.4 and used
> "add_transcript_from_gff3_to_annotations.pl"
> script to bulk load GFF3 file.
> But some loaded CDS coordinates were different from original ones.
> Maybe those were recalculated.
> How can I load original CDS coordinates?
>
> Thanks,
> Yasuhiro
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Question about loading CDS coordinates

Monica Munoz-Torres
Dear Yasuhiro - 

I kindly suggest that you please wait just a little longer before pulling from master. After more discussion within the Apollo development team I made some suggestions for corrections to the patches that were pushed today.

See here for more details:

We will be able to get back to this tomorrow morning (US West Coast and Midwest Time zones).

We are working furiously on it, and will update as soon as it is ready. 

Thanks again. 

cheers, 
~moni. 



On Thu, Oct 6, 2016 at 6:44 PM, 青木康洋 <[hidden email]> wrote:
Thank you.
That helps me a lot.

Yasuhiro

2016-10-07 2:43 GMT+09:00 Nathan Dunn <[hidden email]>:
>
> This is fixed and in master now (thanks Deepak!) if you want to re-clone or
> pull you should pick it up.   The default is what you want so no
> configuration changes will need to be made.
>
>
> Nathan
>
> On Oct 6, 2016, at 9:50 AM, Nathan Dunn <[hidden email]> wrote:
>
>
> By default it should do this since the default apollo variable
> ‘use_cds_for_new_transcripts’ is set to true.   However, we identified a
> bug:
>
> https://github.com/GMOD/Apollo/issues/1297
>
> We should have a fix for this relatively soon (and will repost once its
> merged).
>
> Thanks for bringing it to our attention and sorry for the inconvenience.
>
> Nathan Dunn, PhD
> Berkeley Bioinformatics Open-source Projects (BBOP)
> Genomics Division, Lawrence Berkeley National Laboratory
> [hidden email]
>
>
> On Oct 6, 2016, at 8:20 AM, 青木康洋 <[hidden email]> wrote:
>
> Dear  Apollo team members,
>
> I installed Apollo 2.0.4 and used
> "add_transcript_from_gff3_to_annotations.pl"
> script to bulk load GFF3 file.
> But some loaded CDS coordinates were different from original ones.
> Maybe those were recalculated.
> How can I load original CDS coordinates?
>
> Thanks,
> Yasuhiro
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Question about loading CDS coordinates

nathandunn
Yasuhiro,

We have created a final update for this issue with the code released in master.  After discussing further the updates are as follows:

- when using the “add_transcripts_from_gff3_to_annotations.pl” script, if you use the -X (uppercase) option, CDS’s are imported as-is from the GFF3 (they are not recalculated).  I think this is the only change you needed.

- the default behavior when creating an annotation from evidence (not using the existing script) is to re-calculate the CDS

- to over-ride the default behavior and use evidence as-is without re-calculating, modify the apollo-config.groovy by setting:

     apollo.use_cds_for_new_transcripts = true


Let us know you have any questions / comments or if there is a problem with this.  

Thank you for bringing it to our attention,

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
[hidden email]


On Oct 6, 2016, at 7:00 PM, Monica Munoz-Torres <[hidden email]> wrote:

Dear Yasuhiro - 

I kindly suggest that you please wait just a little longer before pulling from master. After more discussion within the Apollo development team I made some suggestions for corrections to the patches that were pushed today.

See here for more details:

We will be able to get back to this tomorrow morning (US West Coast and Midwest Time zones).

We are working furiously on it, and will update as soon as it is ready. 

Thanks again. 

cheers, 
~moni. 



On Thu, Oct 6, 2016 at 6:44 PM, 青木康洋 <[hidden email]> wrote:
Thank you.
That helps me a lot.

Yasuhiro

2016-10-07 2:43 GMT+09:00 Nathan Dunn <[hidden email]>:
>
> This is fixed and in master now (thanks Deepak!) if you want to re-clone or
> pull you should pick it up.   The default is what you want so no
> configuration changes will need to be made.
>
>
> Nathan
>
> On Oct 6, 2016, at 9:50 AM, Nathan Dunn <[hidden email]> wrote:
>
>
> By default it should do this since the default apollo variable
> ‘use_cds_for_new_transcripts’ is set to true.   However, we identified a
> bug:
>
> https://github.com/GMOD/Apollo/issues/1297
>
> We should have a fix for this relatively soon (and will repost once its
> merged).
>
> Thanks for bringing it to our attention and sorry for the inconvenience.
>
> Nathan Dunn, PhD
> Berkeley Bioinformatics Open-source Projects (BBOP)
> Genomics Division, Lawrence Berkeley National Laboratory
> [hidden email]
>
>
> On Oct 6, 2016, at 8:20 AM, 青木康洋 <[hidden email]> wrote:
>
> Dear  Apollo team members,
>
> I installed Apollo 2.0.4 and used
> "add_transcript_from_gff3_to_annotations.pl"
> script to bulk load GFF3 file.
> But some loaded CDS coordinates were different from original ones.
> Maybe those were recalculated.
> How can I load original CDS coordinates?
>
> Thanks,
> Yasuhiro
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.





--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Question about loading CDS coordinates

青木康洋
Dear Apollo team members,

I appreciate your good work.
Thank you very much.

Yasuhiro

2016-10-08 1:47 GMT+09:00 Nathan Dunn <[hidden email]>:

> Yasuhiro,
>
> We have created a final update for this issue with the code released in
> master.  After discussing further the updates are as follows:
>
> - when using the “add_transcripts_from_gff3_to_annotations.pl” script, if
> you use the -X (uppercase) option, CDS’s are imported as-is from the GFF3
> (they are not recalculated).  I think this is the only change you needed.
>
> - the default behavior when creating an annotation from evidence (not using
> the existing script) is to re-calculate the CDS
>
> - to over-ride the default behavior and use evidence as-is without
> re-calculating, modify the apollo-config.groovy by setting:
>
>      apollo.use_cds_for_new_transcripts = true
>
>
> Let us know you have any questions / comments or if there is a problem with
> this.
>
> Thank you for bringing it to our attention,
>
> Nathan Dunn, PhD
> Berkeley Bioinformatics Open-source Projects (BBOP)
> Genomics Division, Lawrence Berkeley National Laboratory
> [hidden email]
>
>
> On Oct 6, 2016, at 7:00 PM, Monica Munoz-Torres <[hidden email]> wrote:
>
> Dear Yasuhiro -
>
> I kindly suggest that you please wait just a little longer before pulling
> from master. After more discussion within the Apollo development team I made
> some suggestions for corrections to the patches that were pushed today.
>
> See here for more details:
> https://github.com/GMOD/Apollo/issues/1297
> https://github.com/GMOD/Apollo/pull/1298
> https://github.com/GMOD/Apollo/pull/1299
>
> We will be able to get back to this tomorrow morning (US West Coast and
> Midwest Time zones).
>
> We are working furiously on it, and will update as soon as it is ready.
>
> Thanks again.
>
> cheers,
> ~moni.
>
>
>
> On Thu, Oct 6, 2016 at 6:44 PM, 青木康洋 <[hidden email]> wrote:
>>
>> Thank you.
>> That helps me a lot.
>>
>> Yasuhiro
>>
>> 2016-10-07 2:43 GMT+09:00 Nathan Dunn <[hidden email]>:
>> >
>> > This is fixed and in master now (thanks Deepak!) if you want to re-clone
>> > or
>> > pull you should pick it up.   The default is what you want so no
>> > configuration changes will need to be made.
>> >
>> >
>> > Nathan
>> >
>> > On Oct 6, 2016, at 9:50 AM, Nathan Dunn <[hidden email]> wrote:
>> >
>> >
>> > By default it should do this since the default apollo variable
>> > ‘use_cds_for_new_transcripts’ is set to true.   However, we identified a
>> > bug:
>> >
>> > https://github.com/GMOD/Apollo/issues/1297
>> >
>> > We should have a fix for this relatively soon (and will repost once its
>> > merged).
>> >
>> > Thanks for bringing it to our attention and sorry for the inconvenience.
>> >
>> > Nathan Dunn, PhD
>> > Berkeley Bioinformatics Open-source Projects (BBOP)
>> > Genomics Division, Lawrence Berkeley National Laboratory
>> > [hidden email]
>> >
>> >
>> > On Oct 6, 2016, at 8:20 AM, 青木康洋 <[hidden email]> wrote:
>> >
>> > Dear  Apollo team members,
>> >
>> > I installed Apollo 2.0.4 and used
>> > "add_transcript_from_gff3_to_annotations.pl"
>> > script to bulk load GFF3 file.
>> > But some loaded CDS coordinates were different from original ones.
>> > Maybe those were recalculated.
>> > How can I load original CDS coordinates?
>> >
>> > Thanks,
>> > Yasuhiro
>> >
>> >
>> >
>> > This list is for the Apollo Annotation Editing Tool. Info at
>> > http://genomearchitect.org/
>> > If you wish to unsubscribe from the Apollo List: 1. From the address
>> > with
>> > which you subscribed to the list, send a message to [hidden email]
>> > | 2.
>> > In the subject line of your email type: unsubscribe apollo | 3. Leave
>> > the
>> > message body blank.
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > This list is for the Apollo Annotation Editing Tool. Info at
>> > http://genomearchitect.org/
>> > If you wish to unsubscribe from the Apollo List: 1. From the address
>> > with
>> > which you subscribed to the list, send a message to [hidden email]
>> > | 2.
>> > In the subject line of your email type: unsubscribe apollo | 3. Leave
>> > the
>> > message body blank.
>> >
>> >
>>
>>
>>
>>
>>
>> This list is for the Apollo Annotation Editing Tool. Info at
>> http://genomearchitect.org/
>> If you wish to unsubscribe from the Apollo List: 1. From the address with
>> which you subscribed to the list, send a message to [hidden email] | 2.
>> In the subject line of your email type: unsubscribe apollo | 3. Leave the
>> message body blank.
>>
>>
>
>
>
> --
> Mentorship Matters!
> --
> Monica Munoz-Torres, PhD.
> Berkeley Bioinformatics Open-source Projects (BBOP)
> Environmental Genomics and Systems Biology Division
> Lawrence Berkeley National Laboratory
>
> Mailing Address:
> Lawrence Berkeley National Laboratory
> 1 Cyclotron Road Mailstop 977
> Berkeley, CA 94720
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at
> http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with
> which you subscribed to the list, send a message to [hidden email] | 2.
> In the subject line of your email type: unsubscribe apollo | 3. Leave the
> message body blank.
>
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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