GMOD › Chado

Re: genbank to gff3 conversion problem

Classic

List

Threaded

4 messages Options

j_patterson

Re: genbank to gff3 conversion problem

I am getting the same error with this file:
ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/gbs/hs_ref_GRCh37.p5_chr7.gbs.gz

MSG: PROBLEM, SEVERITY==2
no containers possible for SeqFeature of type: CDS; this SF is being placed
at root level
SF [Bio::SeqFeature::Generic=HASH(0x9d548c0)]: CDS; PEG10;
retrotransposon-derived protein PEG10 isoform 3

PEG10 has the ribosomal slippage thing going on. If I change the genbank
file pretending there is no PEG10 slipping the file can be converted.

I think that the slippage situation with PEG10 might not be addresed by the
flattener.

its like: join(94292869..94293825,94293825..94294994)

the frame shifts -1, so the last bp of the first segment is the begining of
the next.

or possibly the genbank file is messed up

It not really a problem for me, but thought it might be worth mentioning in
case it is the unflattener

--
View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/genbank-to-gff3-conversion-problem-tp460065p5443555.html
Sent from the gmod-schema mailing list archive at Nabble.com.

------------------------------------------------------------------------------
Keep Your Developer Skills Current with LearnDevNow!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-d2d
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema

Chris Mungall

Re: genbank to gff3 conversion problem

You're right, there was a problem. I've implemented a fix, seems to work on your example below, and the previous one, will try a few more tests then commit

(Of course this example highlights the insanity of the Unflattener existing at all - the information of which mRNA goes with which CDS is there in a textual description. Will we ever get beyond genbank flat files?)

Umm, can someone remind me how to get my changes back into bioperl? I have master checked out, made changes there, I didn't fork. Can I just commit to master and push or is that bad practice?

Am traveling / at meetings this week so may be next week when this gets done

On Jan 31, 2012, at 3:51 AM, j_patterson wrote:

> I am getting the same error with this file:
> ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/gbs/hs_ref_GRCh37.p5_chr7.gbs.gz
>
> MSG: PROBLEM, SEVERITY==2
> no containers possible for SeqFeature of type: CDS; this SF is being placed
> at root level
> SF [Bio::SeqFeature::Generic=HASH(0x9d548c0)]: CDS; PEG10;
> retrotransposon-derived protein PEG10 isoform 3
>
> PEG10 has the ribosomal slippage thing going on. If I change the genbank
> file pretending there is no PEG10 slipping the file can be converted.
>
> I think that the slippage situation with PEG10 might not be addresed by the
> flattener.
>
> its like: join(94292869..94293825,94293825..94294994)
>
> the frame shifts -1, so the last bp of the first segment is the begining of
> the next.
>
> or possibly the genbank file is messed up
>
> It not really a problem for me, but thought it might be worth mentioning in
> case it is the unflattener
>
> --
> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/genbank-to-gff3-conversion-problem-tp460065p5443555.html
> Sent from the gmod-schema mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
Keep Your Developer Skills Current with LearnDevNow!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-d2d
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema

Fields, Christopher J

Re: genbank to gff3 conversion problem

Chris,

You can push directly back, your github acct is listed on the development team. Let me know if you run into problems with it.

chris (f)

On Jan 31, 2012, at 2:01 AM, Chris Mungall wrote:

>
> You're right, there was a problem. I've implemented a fix, seems to work on your example below, and the previous one, will try a few more tests then commit
>
> (Of course this example highlights the insanity of the Unflattener existing at all - the information of which mRNA goes with which CDS is there in a textual description. Will we ever get beyond genbank flat files?)
>
> Umm, can someone remind me how to get my changes back into bioperl? I have master checked out, made changes there, I didn't fork. Can I just commit to master and push or is that bad practice?
>
> Am traveling / at meetings this week so may be next week when this gets done
>
> On Jan 31, 2012, at 3:51 AM, j_patterson wrote:
>
>> I am getting the same error with this file:
>> ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/gbs/hs_ref_GRCh37.p5_chr7.gbs.gz
>>
>> MSG: PROBLEM, SEVERITY==2
>> no containers possible for SeqFeature of type: CDS; this SF is being placed
>> at root level
>> SF [Bio::SeqFeature::Generic=HASH(0x9d548c0)]: CDS; PEG10;
>> retrotransposon-derived protein PEG10 isoform 3
>>
>> PEG10 has the ribosomal slippage thing going on. If I change the genbank
>> file pretending there is no PEG10 slipping the file can be converted.
>>
>> I think that the slippage situation with PEG10 might not be addresed by the
>> flattener.
>>
>> its like: join(94292869..94293825,94293825..94294994)
>>
>> the frame shifts -1, so the last bp of the first segment is the begining of
>> the next.
>>
>> or possibly the genbank file is messed up
>>
>> It not really a problem for me, but thought it might be worth mentioning in
>> case it is the unflattener
>>
>> --
>> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/genbank-to-gff3-conversion-problem-tp460065p5443555.html
>> Sent from the gmod-schema mailing list archive at Nabble.com.
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

Chris Mungall

Re: genbank to gff3 conversion problem

fix pushed to master

On Jan 31, 2012, at 1:39 PM, Fields, Christopher J wrote:

> Chris,
>
> You can push directly back, your github acct is listed on the development team. Let me know if you run into problems with it.
>
> chris (f)
>
> On Jan 31, 2012, at 2:01 AM, Chris Mungall wrote:
>
>>
>> You're right, there was a problem. I've implemented a fix, seems to work on your example below, and the previous one, will try a few more tests then commit
>>
>> (Of course this example highlights the insanity of the Unflattener existing at all - the information of which mRNA goes with which CDS is there in a textual description. Will we ever get beyond genbank flat files?)
>>
>> Umm, can someone remind me how to get my changes back into bioperl? I have master checked out, made changes there, I didn't fork. Can I just commit to master and push or is that bad practice?
>>
>> Am traveling / at meetings this week so may be next week when this gets done
>>
>> On Jan 31, 2012, at 3:51 AM, j_patterson wrote:
>>
>>> I am getting the same error with this file:
>>> ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/gbs/hs_ref_GRCh37.p5_chr7.gbs.gz
>>>
>>> MSG: PROBLEM, SEVERITY==2
>>> no containers possible for SeqFeature of type: CDS; this SF is being placed
>>> at root level
>>> SF [Bio::SeqFeature::Generic=HASH(0x9d548c0)]: CDS; PEG10;
>>> retrotransposon-derived protein PEG10 isoform 3
>>>
>>> PEG10 has the ribosomal slippage thing going on. If I change the genbank
>>> file pretending there is no PEG10 slipping the file can be converted.
>>>
>>> I think that the slippage situation with PEG10 might not be addresed by the
>>> flattener.
>>>
>>> its like: join(94292869..94293825,94293825..94294994)
>>>
>>> the frame shifts -1, so the last bp of the first segment is the begining of
>>> the next.
>>>
>>> or possibly the genbank file is messed up
>>>
>>> It not really a problem for me, but thought it might be worth mentioning in
>>> case it is the unflattener
>>>
>>> --
>>> View this message in context: http://generic-model-organism-system-database.450254.n5.nabble.com/genbank-to-gff3-conversion-problem-tp460065p5443555.html
>>> Sent from the gmod-schema mailing list archive at Nabble.com.
>>>
>>> ------------------------------------------------------------------------------
>>> Keep Your Developer Skills Current with LearnDevNow!
>>> The most comprehensive online learning library for Microsoft developers
>>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>>> Metro Style Apps, more. Free future releases when you subscribe now!
>>> http://p.sf.net/sfu/learndevnow-d2d
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>

------------------------------------------------------------------------------
Try before you buy = See our experts in action!
The most comprehensive online learning library for Microsoft developers
is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
Metro Style Apps, more. Free future releases when you subscribe now!
http://p.sf.net/sfu/learndevnow-dev2
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema