how to?: save reference sequence edits from command line

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how to?: save reference sequence edits from command line

Cook, Malcolm

Hello,

 

I am able to command-line export all curated gene models from Apollo using supplied groovy script Apollo/docs/web_services/examples/groovy/get_gff3.groovy

 

Is there something analogous for command-line export of all reference sequence edits, as created with “Apollo > Reference Sequence > Right Click > Create Genomic Insertion/Deletion/Substitution”

 

I know how to do this interactively scaffold-by-scaffold using Apollo > Reference Sequence > Right Click > Save Track Data but would like to automake.

 

Ideally, I could parameterize by:

Edit type: { Insertion/Deletion/Substitution}

Sequence: regular expression?

Owner: regular expression?

Justification: regular expression?

 

Thanks,

 

~[hidden email]

 





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RE: how to?: save reference sequence edits from command line

Cook, Malcolm

Doh!

 

I now see that insertions, deletions, substitutions are intermingled with user gene models in the results of get_gff3.groovy script.

 

Rockin’ with Apollo,

 

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Cook, Malcolm
Sent: Sunday, December 03, 2017 3:11 PM
To: [hidden email]
Subject: [apollo] how to?: save reference sequence edits from command line

 

Hello,

 

I am able to command-line export all curated gene models from Apollo using supplied groovy script Apollo/docs/web_services/examples/groovy/get_gff3.groovy

 

Is there something analogous for command-line export of all reference sequence edits, as created with “Apollo > Reference Sequence > Right Click > Create Genomic Insertion/Deletion/Substitution”

 

I know how to do this interactively scaffold-by-scaffold using Apollo > Reference Sequence > Right Click > Save Track Data but would like to automake.

 

Ideally, I could parameterize by:

Edit type: { Insertion/Deletion/Substitution}

Sequence: regular expression?

Owner: regular expression?

Justification: regular expression?

 

Thanks,

 

[hidden email]

 





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.