[InterMine Dev] AIC (Alternative Initiation Codon) mapping as a function in Intermine

Julie Sullivan julie at flymine.org
Fri Feb 19 11:46:01 GMT 2016


Hi Daniel,

1. DATA IN

Were you able to get your data into your mine? In your last email you 
said you were having problems with the InterMine FASTA data source.

Do you have the error messages? Or were you able to get it to work?

2. DATA OUT

It seems like you want to query your mine for sequence data then do some 
further manipulation with a script. Is that right?

Here's our documentation on the web service call you can do to retrieve 
sequence information:

http://iodocs.apps.intermine.org/flymine/docs#/ws-fasta-query/POST/query/results/fasta

That example is querying flymine, but you can just replace FlyMine with 
your local InterMine and the query will work. Provided you've loaded 
sequence information successfully.

So I would think you would use Perl/Python/Whatever to run that query, 
get your sequence data, do whatever manipulation is needed - then write 
the results to a file.

Does that sound sensible? Was that what you had in mind?

Cheers
Julie

On 18/02/16 21:04, davies d.s. (dsd2g13) wrote:
> I need to make Intermine map arbitrarily found sequences of three
> letters to text files of DNA code, that is, I need it to find them in
> the text files at specific locations, and I need it to take the text in
> the particular paragraph after the spot where it has found them, stick
> it to the beginning of the next paragraph minus the paragraph's title,
> and spit the results out in another text file.
> Not only that, but I need it to pick the three letter codons based on
> certain parameters.
> I need it to do this however many times is necessary per gene for a
> whole list of genes
> where 'however many times is necessary' is determined by how many
> criteria-fitting codons there are per gene.
> The resultant text should be displayed on the web page too and it should
> be available for follow-up queries. However, at the moment I can't even
> get it to display any of the data it has.
> www.intermine.org and intermine.readthedocs.org have sort of helped but
> I need more brains to throw at this than fit in my head tonight. My
> deadline to at least know how to do this is Saturday, sorry it's a bit
> short notice but it is part of my third year dissertation as well as a
> longer term project for Vulpine Designs Unlimited.
>
>
> Daniel Davies
> Third year student, BSc Biochemistry
>
> Founder,
> The Dorset Constructorium
> http://www.constructorium.org
>
> Founder & CEO,
> Vulpine Designs Unlimited
> http://www.vulpinedesigns.co.uk
> Freedom of Form: an evolution revolution
>
>
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