AIC (Alternative Initiation Codon) mapping as a function in Intermine

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AIC (Alternative Initiation Codon) mapping as a function in Intermine

davies d.s. (dsd2g13)

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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Re: AIC (Alternative Initiation Codon) mapping as a function in Intermine

Julie Sullivan
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
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
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Re: AIC (Alternative Initiation Codon) mapping as a function in Intermine

davies d.s. (dsd2g13)
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 <[hidden email]>
Sent: 19 February 2016 11:46
To: davies d.s. (dsd2g13)
Cc: [hidden email]
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
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
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Re: AIC (Alternative Initiation Codon) mapping as a function in Intermine

Justin Clark-Casey
Hi Dan,

The query builder is the way someone would usually build a complex query.  Once one is built, then at the bottom middle of the page there are code generation
links (Perl, Python, Java, etc.) that will generate code that can execute the same code via the InterMine webservices.

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 24/02/16 13:04, davies d.s. (dsd2g13) wrote:

> 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 <[hidden email]>
> Sent: 19 February 2016 11:46
> To: davies d.s. (dsd2g13)
> Cc: [hidden email]
> 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
>> [hidden email]
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev