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

davies d.s. (dsd2g13) dsd2g13 at soton.ac.uk
Wed Feb 24 13:04:37 GMT 2016


Hi Julie

Thanks for your reply and sorry I didn't get back to you sooner.
I have managed to get Intermine to load a list of the data listed by its Ensembl identifiers from the FASTA headers, as yet without any of the comments from those headers. Each Ensembl identifier comes with a link to the FASTA sequence stored in the clob for that particular header. So in a sense, yes I was able to get some data into the mine, although I am not sure what additional data I need to put in there with it in order to get meaningful search results, particularly for my intended goals.

Before reading your email I had a prod at Templates and the Query Builder, as I wondered whether they can be used to build the complex query required with the appropriate pre-configuration of my mine. A separate script is something I want to consider if that is not possible, code-efficient or practical.

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

________________________________________
From: Julie Sullivan <julie at flymine.org>
Sent: 19 February 2016 11:46
To: davies d.s. (dsd2g13)
Cc: dev at intermine.org
Subject: Re: [InterMine Dev] AIC (Alternative Initiation Codon) mapping as a function in Intermine

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
>
>
> _______________________________________________
> dev mailing list
> dev at intermine.org
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>



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