Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

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Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

Loraine Guéguen
Hi,

Remained unanswered one year ago, I try my luck again:

Does anybody work with both Apollo and Pathway tools ? How do you handle
the conversion from GFF3 (Apollo output) to GenBank (input format for
Pathway Tools) ?

Thanks for your help.

Loraine Guéguen


--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

Joshua Orvis
I wrote this converter, but it expects spec-following GFF3.  I haven't tested it with Apollo output, but would be glad to if you wanted to send me yours.




On Tue, Jan 16, 2018 at 9:00 AM, Loraine Guéguen <[hidden email]> wrote:
Hi,

Remained unanswered one year ago, I try my luck again:

Does anybody work with both Apollo and Pathway tools ? How do you handle the conversion from GFF3 (Apollo output) to GenBank (input format for Pathway Tools) ?

Thanks for your help.

Loraine Guéguen


--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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: Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

Loraine Guéguen
thanks!

Le 16/01/2018 16:04, Joshua Orvis a écrit :
I wrote this converter, but it expects spec-following GFF3.  I haven't tested it with Apollo output, but would be glad to if you wanted to send me yours.




On Tue, Jan 16, 2018 at 9:00 AM, Loraine Guéguen <[hidden email]> wrote:
Hi,

Remained unanswered one year ago, I try my luck again:

Does anybody work with both Apollo and Pathway tools ? How do you handle the conversion from GFF3 (Apollo output) to GenBank (input format for Pathway Tools) ?

Thanks for your help.

Loraine Guéguen


--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a moz-do-not-send="true" href="tel:%2B%2B33%20%280%292%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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. 


-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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: Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

E. Rasche
In reply to this post by Joshua Orvis
Just for comparison/second data point, I wrote this one at my old job,
but it has a lot of custom hacks for weird phage stuff we did. Still
should work in general as well.

https://github.com/TAMU-CPT/galaxy-tools/blob/master/tools/gff3/gff2gb.py


On 2018-01-16, Joshua Orvis wrote:

> I wrote this converter, but it expects spec-following GFF3.  I haven't
> tested it with Apollo output, but would be glad to if you wanted to send me
> yours.
>
> https://github.com/jorvis/biocode/blob/master/genbank/convert_gff3_to_gbk.py
>
>
>
> On Tue, Jan 16, 2018 at 9:00 AM, Loraine Guéguen <
> [hidden email]> wrote:
>
> > Hi,
> >
> > Remained unanswered one year ago, I try my luck again:
> >
> > Does anybody work with both Apollo and Pathway tools ? How do you handle
> > the conversion from GFF3 (Apollo output) to GenBank (input format for
> > Pathway Tools) ?
> >
> > Thanks for your help.
> >
> > Loraine Guéguen
> >
> >
> > --
> > Loraine Guéguen
> >
> > UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> > Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
> >
> > Station Biologique de Roscoff - CNRS / Sorbonne Université
> > Place Georges Teissier - CS 90074
> > 29688 Roscoff cedex
> > tel: ++33 (0)2 98 29 56 46 (interne : 415)
> > http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
> > http://abims.sb-roscoff.fr/
> >
> >
> >
> >
> >
> > 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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Re: Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

nathandunn

Loraine, 

Let us know how these work for eukaryotes.  The Apollo GFF3 should be compliant with the GFF3 standard, but if there are issues with the format during conversion, please let us know.

I opened this issue up  as folks had also requested other conversions that only exist as per as written (in this case gff3 -> tbl -> asn for NCBI submission) .  


Nathan

On Jan 16, 2018, at 11:29 AM, E. Rasche <[hidden email]> wrote:

Just for comparison/second data point, I wrote this one at my old job,
but it has a lot of custom hacks for weird phage stuff we did. Still
should work in general as well.

https://github.com/TAMU-CPT/galaxy-tools/blob/master/tools/gff3/gff2gb.py


On 2018-01-16, Joshua Orvis wrote:
I wrote this converter, but it expects spec-following GFF3.  I haven't
tested it with Apollo output, but would be glad to if you wanted to send me
yours.

https://github.com/jorvis/biocode/blob/master/genbank/convert_gff3_to_gbk.py



On Tue, Jan 16, 2018 at 9:00 AM, Loraine Guéguen <
[hidden email]> wrote:

Hi,

Remained unanswered one year ago, I try my luck again:

Does anybody work with both Apollo and Pathway tools ? How do you handle
the conversion from GFF3 (Apollo output) to GenBank (input format for
Pathway Tools) ?

Thanks for your help.

Loraine Guéguen


--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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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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: Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

Joshua Orvis
Yes, please do.  I'll be happy to fix the one in biocode if you find any issues.

JO

On Tue, Jan 16, 2018 at 3:28 PM, Nathan Dunn <[hidden email]> wrote:

Loraine, 

Let us know how these work for eukaryotes.  The Apollo GFF3 should be compliant with the GFF3 standard, but if there are issues with the format during conversion, please let us know.

I opened this issue up  as folks had also requested other conversions that only exist as per as written (in this case gff3 -> tbl -> asn for NCBI submission) .  


Nathan


On Jan 16, 2018, at 11:29 AM, E. Rasche <[hidden email]> wrote:

Just for comparison/second data point, I wrote this one at my old job,
but it has a lot of custom hacks for weird phage stuff we did. Still
should work in general as well.

https://github.com/TAMU-CPT/galaxy-tools/blob/master/tools/gff3/gff2gb.py


On 2018-01-16, Joshua Orvis wrote:
I wrote this converter, but it expects spec-following GFF3.  I haven't
tested it with Apollo output, but would be glad to if you wanted to send me
yours.

https://github.com/jorvis/biocode/blob/master/genbank/convert_gff3_to_gbk.py



On Tue, Jan 16, 2018 at 9:00 AM, Loraine Guéguen <
[hidden email]> wrote:

Hi,

Remained unanswered one year ago, I try my luck again:

Does anybody work with both Apollo and Pathway tools ? How do you handle
the conversion from GFF3 (Apollo output) to GenBank (input format for
Pathway Tools) ?

Thanks for your help.

Loraine Guéguen


--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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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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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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: Tool to convert GFF3 to GBK ? (in order to use Apollo output as input for Pathway Tools)

Loraine Guéguen
Thanks !



Le 16/01/2018 22:34, Joshua Orvis a écrit :
Yes, please do.  I'll be happy to fix the one in biocode if you find any issues.

JO

On Tue, Jan 16, 2018 at 3:28 PM, Nathan Dunn <[hidden email]> wrote:

Loraine, 

Let us know how these work for eukaryotes.  The Apollo GFF3 should be compliant with the GFF3 standard, but if there are issues with the format during conversion, please let us know.

I opened this issue up  as folks had also requested other conversions that only exist as per as written (in this case gff3 -> tbl -> asn for NCBI submission) .  


Nathan


On Jan 16, 2018, at 11:29 AM, E. Rasche <[hidden email]> wrote:

Just for comparison/second data point, I wrote this one at my old job,
but it has a lot of custom hacks for weird phage stuff we did. Still
should work in general as well.

https://github.com/TAMU-CPT/galaxy-tools/blob/master/tools/gff3/gff2gb.py


On 2018-01-16, Joshua Orvis wrote:
I wrote this converter, but it expects spec-following GFF3.  I haven't
tested it with Apollo output, but would be glad to if you wanted to send me
yours.

https://github.com/jorvis/biocode/blob/master/genbank/convert_gff3_to_gbk.py



On Tue, Jan 16, 2018 at 9:00 AM, Loraine Guéguen <
[hidden email]> wrote:

Hi,

Remained unanswered one year ago, I try my luck again:

Does anybody work with both Apollo and Pathway tools ? How do you handle
the conversion from GFF3 (Apollo output) to GenBank (input format for
Pathway Tools) ?

Thanks for your help.

Loraine Guéguen


--
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: <a moz-do-not-send="true" href="tel:+33%202%2098%2029%2056%2046" value="+33298295646" target="_blank">++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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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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. 


-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS / Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/





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.