fasta domload

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fasta domload

ADRIENNE BRELAND
Hi, 
   Is there any way to allow fatsta sequences to be downloaded from the a linked out page using cgi scripting?

Thanks
Adrienne

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Re: fasta domload

Scott Cain
Hi Adrienne,

Could you be a little more specific?  Given the somewhat vague nature of your question, I'm inclined to say "yes" (because lots of things are possible); what is it you want users to be able to do?

Scott



On Wed, Nov 27, 2013 at 1:13 PM, ADRIENNE BRELAND <[hidden email]> wrote:
Hi, 
   Is there any way to allow fatsta sequences to be downloaded from the a linked out page using cgi scripting?

Thanks
Adrienne

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Scott Cain, Ph. D.                                   scott at scottcain dot net
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Ontario Institute for Cancer Research

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Re: fasta domload

Scott Cain
Hi Adrienne,

Sorry I missed this from last week; always keep the GBrowse mailing list cc'ed so it's visible to everybody on the list.

I would say if you modified gbrowse_details to do something then you are perhaps not an expert, but you're no novice either :-)  

It sounds like what you would like to do is to have a user click on a transcript feature and then have the cgi do the splicing of the genomic sequence to create a spliced transcript sequence, that the user could then copy to do with what he wants.  Is that what you mean?

The gbrowse_details page can't do that, nor do I think there is a plugin that comes with GBrowse that does either, but with a little bit of BioPerl magic, you should be able to.  BioPerl SeqFeature objects have a spliced_seq method that takes the exon/CDS sections and puts them together for you, so if you feed it a transcript or mRNA object (which you'd get inside the gbrowse_details page) with exons or CDS child features, calling spliced_seq on the parent feature should give you the sequence of the mature transcript.  (How's that for hand waving? :)

Scott



On Tue, Dec 10, 2013 at 12:35 AM, An <[hidden email]> wrote:
Hi Scott, 
    Thanks for the reply.  I'm not a cgi expert first of all. I have modified the gbrowse_details cgi script to show a table and images for transcripts that we display when they are clicked  on. I would also like to display a download button  where the user can download the coding regions of the transcripts fasta sequence. Currently, I am displaying the entire fasta segment and a user would have to copy an paste from the page. Can we use the decorated fasta plugin on another page?
      I hope this makes sense!

Adrienne

Sent from my iPad

On Dec 9, 2013, at 7:51 PM, Scott Cain <[hidden email]> wrote:

Hi Adrienne,

Could you be a little more specific?  Given the somewhat vague nature of your question, I'm inclined to say "yes" (because lots of things are possible); what is it you want users to be able to do?

Scott



On Wed, Nov 27, 2013 at 1:13 PM, ADRIENNE BRELAND <[hidden email]> wrote:
Hi, 
   Is there any way to allow fatsta sequences to be downloaded from the a linked out page using cgi scripting?

Thanks
Adrienne

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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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