[apollo] .game file format conversion to .gff

[Sabrina Legoueix]

Dear all,


I would like to convert a .game file to a .gff or tabular file.


Could you please tell me if such a script exists? If not, could you please provide me some advices on how to do so?


Thanks in advance.


Best regards,


Sabrina




Sabrina LEGOUEIX RODRIGUEZ
Responsable Plateau Bioinformatique

Tél. : [phone]
***@inra.fr<mailto:[MAIL]>
www.toulouse-white-biotechnology.com<http://www.toulouse-white-biotechnology.com/>


TWB - Parc technologique du canal * Bâtiment NAPA CENTER B * 3, rue Ariane *
31520 Ramonville Saint-Agne

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[Deepak Unni]

Hi Sabrina,

The GAME XML format used to be compatible with Desktop Apollo, and since
has not been used in favor of newer file formats.
We are checking to see if there are any existing scripts that can convert a
GAME XML format to GFF3.

Meanwhile, here is the schema description for GAME XML format:
http://chopsticks.lbl.gov/current/game.rng.txt
Perhaps this can serve as a starting point for interpreting the schema of
your XML and converting it into a GFF3.

Cheers,

Deepak

Post by Sabrina Legoueix
Dear all,
I would like to convert a .game file to a .gff or tabular file.
Could you please tell me if such a script exists? If not, could you
please provide me some advices on how to do so?
Thanks in advance.
Best regards,
Sabrina
*Sabrina LEGOUEIX RODRIGUEZ*
Responsable Plateau Bioinformatique
Tél. : [phone] <+33%205%2061%2028%2057%2092>
www.toulouse-white-biotechnology.com
TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane
•
31520 Ramonville Saint-Agne
Ce message et ses piÚces jointes sont strictement personnels. Ils peuvent
contenir des informations confidentielles. Si vous avez reçu ce message par
erreur, merci d'en avertir l'expéditeur et de détruire le message et les
documents joints. Toute utilisation des informations reçues par erreur est
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contain confidential information. If you have received this message in
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[Suzanna Lewis]

AFAIK no such scripts remain. Shouldn't be too difficult to put one
together though.

Post by Deepak Unni
Hi Sabrina,
The GAME XML format used to be compatible with Desktop Apollo, and since
has not been used in favor of newer file formats.
We are checking to see if there are any existing scripts that can convert
a GAME XML format to GFF3.
http://chopsticks.lbl.gov/current/game.rng.txt
Perhaps this can serve as a starting point for interpreting the schema of
your XML and converting it into a GFF3.
Cheers,
Deepak
On Mon, Dec 5, 2016 at 10:08 AM, Sabrina Legoueix <

Post by Sabrina Legoueix
Dear all,
I would like to convert a .game file to a .gff or tabular file.
Could you please tell me if such a script exists? If not, could you
please provide me some advices on how to do so?
Thanks in advance.
Best regards,
Sabrina
*Sabrina LEGOUEIX RODRIGUEZ*
Responsable Plateau Bioinformatique
Tél. : [phone] <+33%205%2061%2028%2057%2092>
www.toulouse-white-biotechnology.com
TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue
Ariane •
31520 Ramonville Saint-Agne
Ce message et ses piÚces jointes sont strictement personnels. Ils peuvent
contenir des informations confidentielles. Si vous avez reçu ce message par
erreur, merci d'en avertir l'expéditeur et de détruire le message et les
documents joints. Toute utilisation des informations reçues par erreur est
interdite. This message and the attachments are strictly personal. They may
contain confidential information. If you have received this message in
error, please notify the sender and delete the message and the attachments.
Any use of this communication received in error is prohibited.
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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia
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[Fields, Christopher J]

There is a BioPerl Bio::SeqIO parser:

https://github.com/bioperl/bioperl-live/blob/master/Bio/SeqIO/game.pm

Not sure how complete it is but might be worth a look.

Chris

Sent from my iPhone

On Dec 8, 2016, at 3:12 PM, Suzanna Lewis <***@lbl.gov<mailto:***@lbl.gov>> wrote:

AFAIK no such scripts remain. Shouldn't be too difficult to put one together though.


On Mon, Dec 5, 2016 at 12:01 PM, Deepak Unni <***@gmail.com<mailto:***@gmail.com>> wrote:
Hi Sabrina,

The GAME XML format used to be compatible with Desktop Apollo, and since has not been used in favor of newer file formats.
We are checking to see if there are any existing scripts that can convert a GAME XML format to GFF3.

Meanwhile, here is the schema description for GAME XML format: http://chopsticks.lbl.gov/current/game.rng.txt<https://urldefense.proofpoint.com/v2/url?u=http-3A__chopsticks.lbl.gov_current_game.rng.txt&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=tDGDphAO6NEimtzLSSmQFGvp83Nv4of3Q091GUeBRjE&m=2VF6Xm4pOSFHNbimB5qgxfDghS8FfPtlKlKjo6r9fHY&s=424Docxw_pwfuxXFuJTWQFehmCU0BvRFjzL_48wbDsM&e=>
Perhaps this can serve as a starting point for interpreting the schema of your XML and converting it into a GFF3.

Cheers,

Deepak

On Mon, Dec 5, 2016 at 10:08 AM, Sabrina Legoueix <***@inra.fr<mailto:***@inra.fr>> wrote:

Dear all,


I would like to convert a .game file to a .gff or tabular file.


Could you please tell me if such a script exists? If not, could you please provide me some advices on how to do so?


Thanks in advance.


Best regards,


Sabrina




Sabrina LEGOUEIX RODRIGUEZ
Responsable Plateau Bioinformatique

Tél. : [phone]<tel:+33%205%2061%2028%2057%2092>
***@inra.fr<mailto:[MAIL]>
www.toulouse-white-biotechnology.com<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.toulouse-2Dwhite-2Dbiotechnology.com_&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=tDGDphAO6NEimtzLSSmQFGvp83Nv4of3Q091GUeBRjE&m=2VF6Xm4pOSFHNbimB5qgxfDghS8FfPtlKlKjo6r9fHY&s=GNZXPJO1XN7kfDNri_w4UyFqgF4xkaNKDnnwo8qRSRc&e=>


TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane •
31520 Ramonville Saint-Agne

Ce message et ses pièces jointes sont strictement personnels. Ils peuvent contenir des informations confidentielles. Si vous avez reçu ce message par erreur, merci d'en avertir l'expéditeur et de détruire le message et les documents joints. Toute utilisation des informations reçues par erreur est interdite. This message and the attachments are strictly personal. They may contain confidential information. If you have received this message in error, please notify the sender and delete the message and the attachments. Any use of this communication received in error is prohibited.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__genomearchitect.org_&d=DQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=tDGDphAO6NEimtzLSSmQFGvp83Nv4of3Q091GUeBRjE&m=2VF6Xm4pOSFHNbimB5qgxfDghS8FfPtlKlKjo6r9fHY&s=6KiIXvtgK7JSfusHFnFdZa93pOReDQlYUmPq9Z0TAlo&e=>
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--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia




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