Re: [BioMart Users] perl API and transcript flanks
Syed Haider <sah84 <at> cam.ac.uk>
2012-07-05 20:11:02 GMT
Hi Francesco,
please replace your registry file with the one enclosed, and see if that
helps.
Syed
On 05/07/2012 13:12, Francesco Marass wrote:
> Dear Syed,
>
> Thank you for your reply.
>
> Here are three queries and the size of their output:
>
>
> ## SCENARIO 1 -- Transcript and no flanking regions
>
> $query =
> BioMart::Query->new("registry"=>$registry,"virtualSchemaName"=>"default");
> $query->setDataset("hsapiens_gene_ensembl");
> $query->addFilter("ensembl_transcript_id",[$ensembl_id]);
> $query->addAttribute("ensembl_transcript_id");
> $query->addAttribute("transcript_exon_intron");
> $query->addAttribute("strand");
> $query->formatter("FASTA");
>
> # execute query
> $query_run=BioMart::QueryRunner->new();
> $query_run->uniqueRowsOnly(1);
> $query_run->execute($query);
>
> # save results
> open($fho,'>',"mart_q3_results.txt");
> $query_run->printResults($fho);
> close($fho);
>
>
> ## OUTPUT 1
> $ wc mart_q3_results.txt
> 319 319 19395 mart_q3_results.txt
>
>
>
> ## SCENARIO 2 -- Transcript and flanking regions
>
> $query =
> BioMart::Query->new("registry"=>$registry,"virtualSchemaName"=>"default");
> $query->setDataset("hsapiens_gene_ensembl");
> $query->addFilter("ensembl_transcript_id",[$ensembl_id]);
> $query->addFilter("downstream_flank",["100"]);
> $query->addFilter("upstream_flank",["100"]);
> $query->addAttribute("ensembl_transcript_id");
> $query->addAttribute("transcript_exon_intron");
> $query->addAttribute("strand");
> $query->formatter("FASTA");
>
> # execute query
> $query_run=BioMart::QueryRunner->new();
> $query_run->uniqueRowsOnly(1);
> $query_run->execute($query);
>
> # save results
> open($fho,'>',"mart_q3_results2.txt");
> $query_run->printResults($fho);
> close($fho);
>
>
> ## OUTPUT 2
> $ wc mart_q3_results2.txt
> 319 319 19395 mart_q3_results2.txt
>
>
>
> ## SCENARIO 3 -- Just flanks
>
> $query =
> BioMart::Query->new("registry"=>$registry,"virtualSchemaName"=>"default");
> $query->setDataset("hsapiens_gene_ensembl");
> $query->addFilter("upstream_flank", ["100"]);
> $query->addFilter("ensembl_transcript_id", ["ENST00000396473"]);
> $query->addAttribute("ensembl_gene_id");
> $query->addAttribute("ensembl_transcript_id");
> $query->addAttribute("transcript_flank");
> $query->formatter("FASTA");
>
> # execute query
> $query_run=BioMart::QueryRunner->new();
> $query_run->uniqueRowsOnly(1);
> $query_run->execute($query);
>
> # save results
> open($fho,'>',"mart_q3_results3.txt");
> $query_run->printResults($fho);
> close($fho);
>
>
> ## OUTPUT 3
> $ wc mart_q3_results3.txt
> 0 0 0 mart_q3_results3.txt
>
>
> As you can see, if a ask for a transcript I correctly receive what I want
> (#1). If I ask for a transcript with 100bp on either side (#2), I receive
> the same transcript as in scenario #1, indicating that the
> downstream_flank and upstream_flank conditions are ignored. If I only ask
> for the 100bp (upstream) flanking a transcript, I get nothing (#3).
>
>
>
> My ensembl.xml is the following:
>
> <MartRegistry>
> <MartURLLocation
> name = "ensembl"
> displayName = "ensembl"
> host = "www.biomart.org"
> port = "80"
> visible = "1"
> default = "0"
> includeDatasets = "hsapiens_gene_ensembl"
> martUser = ""
> />
> <MartURLLocation
> name = "sequence"
> displayName = "sequence"
> host = "www.biomart.org"
> port = "80"
> visible = "1"
> default = "0"
> includeDatasets = "hsapiens_genomic_sequence"
> martUser = ""
> />
> <MartURLLocation
> database = "snp_mart_67a"
> displayName = "ENSEMBL VARIATION 67 (SANGER UK)"
> host = "www.biomart.org"
> includeDatasets = "hsapiens_structvar,hsapiens_snp_som,hsapiens_snp"
> martUser = ""
> name = "snp"
> path = "/biomart/martservice"
> port = "80"
> visible = "1"
> default = "0"
> />
> </MartRegistry>
>
>
>
>
> Best,
>
> Francesco
>
>
>
>
> On 04/07/2012 20:20, "Syed Haider" <sah84 <at> cam.ac.uk> wrote:
>
>> Francesco,
>>
>> a- please explain what you mean by "flanks can never be retrieved" ?
>> b- whats your ensembl.xml file like ?
>>
>> Syed
>>
>> On 04/07/2012 12:33, Francesco Marass wrote:
>>> Hello,
>>>
>>> I am trying to retrieve a transcript sequence using the BioMart perl
>>> API, and I am also interested in the 100bp flanking the transcript.
>>>
>>> When I use the Ensembl BioMart web page, everything works fine. However,
>>> using the perl code automatically generated by the online query (see
>>> below), flanks can never be retrieved. Ensembl's HelpDesk redirected me
>>> to BioMart, where the problem allegedly lies.
>>>
>>> Can someone explain how to retrieve flanking regions?
>>>
>>> Thank you,
>>>
>>> Francesco Marass
>>>
>>>
>>> ###
>>> # An example script demonstrating the use of BioMart API.
>>> # This perl API representation is only available for configuration
>>> versions >= 0.5
>>> use strict;
>>> use BioMart::Initializer;
>>> use BioMart::Query;
>>> use BioMart::QueryRunner;
>>>
>>> my $confFile = "ensembl.xml";
>>> #
>>> # NB: change action to 'clean' if you wish to start a fresh
>>> configuration
>>> # and to 'cached' if you want to skip configuration step on subsequent
>>> runs from the same registry
>>> #
>>>
>>> my $action='cached';
>>> my $initializer = BioMart::Initializer->new('registryFile'=>$confFile,
>>> 'action'=>$action);
>>> my $registry = $initializer->getRegistry;
>>>
>>>
>>> my $query =
>>>
>>> BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default')
>>> ;
>>>
>>> $query->setDataset("hsapiens_gene_ensembl");
>>> $query->addFilter("downstream_flank", ["100"]);
>>> $query->addFilter("upstream_flank", ["100"]);
>>> $query->addFilter("ensembl_transcript_id", ["ENST00000478798"]);
>>> $query->addAttribute("ensembl_gene_id");
>>> $query->addAttribute("ensembl_transcript_id");
>>> $query->addAttribute("transcript_exon_intron");
>>>
>>> $query->formatter("FASTA");
>>>
>>> my $query_runner = BioMart::QueryRunner->new();
>>>
>>> $query_runner->execute($query);
>>> $query_runner->printHeader();
>>> $query_runner->printResults();
>>> $query_runner->printFooter();
>>>
>>> ###
>>>
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>
>
> NOTICE AND DISCLAIMER
> This e-mail (including any attachments) is intended for the above-named person(s). If you are not the
intended recipient, notify the sender immediately, delete this email from your system and do not
disclose or use for any purpose.
>
> We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to
ensure that this email and attachments are free from any virus, but it remains your responsibility to
ensure that viruses do not adversely affect you.
> Cancer Research UK
> Registered in England and Wales
> Company Registered Number: 4325234.
> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.
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