Thank you, Syed. That seems to have solved the problem. Francesco
On 05/07/2012 21:11, "Syed Haider" <[email protected]> wrote: >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" <[email protected]> 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(); >>>> >>>> ### >>>> >>>> NOTICE AND DISCLAIMER >>>> This e-mail (including any attachments) is intended for the >>>>above-named >>>> person(s). 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