biomart-perl's People
Contributors
Watchers
biomart-perl's Issues
Actual releases requests
We would like to make biomart-perl available on our cluster but this requires actual version releases and not pulling branches. Do you foresee this possibility anytime soon?
Wrong peptide sequence if codons originate from two exons
Using the cvs/release-0_7 branch of biomart-perl I got this wrong and wrong formatted fasta output:
>ENSMUST00000117386.2
MGAEEEVQVTLAGGAPWGFRLQGGTEQRKPLQVSKNCNAQKASRRKA*RRQEPNAGPLHPC*QQPPTLTPRGCLCLRSGGREPRSTP**VLGPQLGQEQRRRTASPQRVSRSWTRRPSQTPAALLINPTGTAPI*TWSWLGLA*AQQRVRTLDWEGS*VRSLGEGSSSLNSSASG*PPAPRSWLRWAQQLCLMGRVCSPHLEHRVLPQRQLCSHSALCRSLQSALPPSSRMVEPPS
LHQVSLTGQRGLLPQVYKGKGQVPPQ*FSGPWPLRR*MKAWGALAPPRPPSQPLHRGPPLCPASPQWFPATRRSLGLLAAPNAPLVL*PLPVPCTSQPQAGLLHQEAPQNRPLLLALLP*PPPLPSSCPLH*ETLRARRRRAPRSPSLPAFGSSASLCRLPAPASCRRLGAGAPASRCSGLGRKRRRTRPTR
SCCH*CRTWMKNLGRAVRNLVRRRTL*ASGLKPVTSCSH*GAGVTRPCLKYHRKPRLQWLPKLHPLQRLRLHLPWLLNLGREGSLMG**MDRPRWWESLSRQGCKGGAGSYLPNGRAVPIGTWWKLHLALALIQAFALEVLLPHPHCPH
PGNTHPTSVPHLLLLTTHFSHPFFPKLPELSPIRLNPRGLG*PLSRVSRPWISCDISHTNLKRPCFVLMRVLQLLAPLQGLPKLPEFRRSADFPLLHPSPLQ
SPWLPLCLSPERLPPWTNPFGGQSWPQPLSLTQTIKSLSGALLPLPVPVVSK*PGPGSQPPEQGCRPMSGGLGQGTS
>ENSMUST00000057090.12
MGAEEEVQVTLAGGAPWGFRLQGGTEQRKPLQNCNAQKASRRKA*RRQEPNAGPLHPC*QQPPTLTPRGCLCLRSGGREPRSTP**VLGPQLGQEQRRRTASPQRVSRSWTRRPSQTPAALLINPTGTAPI*TWSWLGLA*AQQRVRTLDWEGS*VRSLGEGSSSLNSSASG*PPAPRSWLRWAQQLCLMGRVCSPHLEHRVLPQRQLCSHSALCRSLQSALPPSSRMVEPPS
LHQVSLTGQRGLLPQVYKGKGQVPPQ*FSGPWPLRR*MKAWGALAPPRPPSQPLHRGPPLCPASPQWFPATRRSLGLLAAPNAPLVL*PLPVPCTSQPQAGLLHQEAPQNRPLLLALLP*PPPLPSSCPLH*ETLRARRRRAPRSPSLPAFGSSASLCRLPAPASCRRLGAGAPASRCSGLGRKRRRTRPTR
SCCH*CRTWMKNLGRAVRNLVRRRTL*ASGLKPVTSCSH*GAGVTRPCLKYHRKPRLQWLPKLHPLQRLRLHLPWLLNLGREGSLMG**MDRPRWWESLSRQGCKGGAGSYLPNGRAVPIGTWWKLHLALALIQAFALEVLLPHPHCPH
PGNTHPTSVPHLLLLTTHFSHPFFPKLPELSPIRLNPRGLG*PLSRVSRPWISCDISHTNLKRPCFVLMRVLQLLAPLQGLPKLPEFRRSADFPLLHPSPLQ
SPWLPLCLSPERLPPWTNPFGGQSWPQPLSLTQTIKSLSGALLPLPVPVVSK*PGPGSQPPEQGCRPMSGGLGQGTS
>ENSMUST00000119483.2
METTIQEPLGQASCDKAPAPELQDPFYAELQRAESLQEKSVKEARTKCRTIASLLTAAPN
PHSKGVLMFKKRRQRAKKYTLVSFGAAAGTGTEEEDGIPPTSESELDEETFSDARSLTNQ
SDWDSPYLDMELARAGLGTAESQNSGLGGQLSEVSGRGVQLFEQQRQRVASSSQELAQVG
PAAMLNGQSLQSPPRAQSAPPEAAVLPLSPLSVPAVSPTPFFPDGGAPIPAPSIFNRSAR
PFTPGLQGQRSGTTSVIFRPLAPKKVNEGLGSTSPAPSPFAAPPQGPTPLPSFTTVVPSH
TPVSGASSSTQRSSGPVTATSSLYIPAPSRPVTPGGAPEPPTPPSAAAMTSTASIFLSTP
LRNSARPEAPGPAVPEPASVREQRISVPAARTGILQEARRRGTRKQMFRPGKEETKNSPN
PELLSLVQNLDEKPRAGGAESGPEEDALSLGAEACNFMQPLGGRSYKTLPQVSPKTPPPM
APKTPPPTTPKTPPPVAPKPGSRGLLDGLVNGSTPMVGIPEPPRLQGRGGELFAKRQSRA
DRYVVEATSGSSLNPGLRPRSPSPTPSLPPSWKYSPNIRAPPPIAYNPLLSPFFPQAART
LPNKAQSQGPRVTPKQGIKALDFMRHQPYQLKTAMFCFDEGSSTPGPTSGPPKTARVQEI
RRFSTPAPQPTAEPLAPTVLVPRAATTLDEPIWRAELASTPVPNPDHQESLRSFAAAPSS
CGFQVARPRFSATRTGLQAHVWRPGAGHQ*
by running this code
#!/usr/bin/env perl
use strict;
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $confFile = "~/biomart-perl/conf/martURLLocation.xml";
my $action='clean';
my $initializer = BioMart::Initializer->new('registryFile'=>$confFile, 'action'=>$action);
my $registry = $initializer->getRegistry;
my $query = BioMart::Query->new('registry'=>$registry,'virtualSchemaName'=>'default');
$query->setDataset("mmusculus_gene_ensembl");
$query->addFilter("ensembl_gene_id", ["ENSMUSG00000039376"]);
$query->addAttribute("ensembl_transcript_id_version");
$query->addAttribute("peptide");
$query->formatter("FASTA");
my $query_runner = BioMart::QueryRunner->new();
$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
In this gene ENSMUSG00000039376 there are codons located on two excons.
Running the above example on https://www.ensembl.org/biomart/martview will return the correct fasta output.
Example run fails
Hi,
I was trying to use the Perl API following the instruction at this link:
https://www.ensembl.org/info/data/biomart/biomart_perl_api.html
I used the proposed example and followed the step one by one and I don't think things are working correctly. Could it be that I'm doing something wrong or is it that the API is not really working anymore?
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 = "../conf/martURLLocation.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 $action='clean';
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("ensembl_gene_id", ["ENSG00000139618"]);
$query->addAttribute("ensembl_gene_id");
$query->addAttribute("ensembl_transcript_id");
$query->addAttribute("hgnc_symbol");
$query->addAttribute("uniprotswissprot");
$query->formatter("TSV");
my $query_runner = BioMart::QueryRunner->new();
############################## GET COUNT ############################
# $query->count(1);
# $query_runner->execute($query);
# print $query_runner->getCount();
#####################################################################
############################## GET RESULTS ##########################
# to obtain unique rows only
# $query_runner->uniqueRowsOnly(1);
$query_runner->execute($query);
$query_runner->printHeader();
$query_runner->printResults();
$query_runner->printFooter();
#####################################################################
I get a weird behaviour
Connection parameters of [Ensembl Genes 99] [ OK ]
Connection parameters of [Mouse strains 99] [ OK ]
Connection parameters of [Sequence] [ OK ]
Connection parameters of [Ontology] [ OK ]
Connection parameters of [Genomic features 99] [ OK ]
Connection parameters of [Ensembl Variation 99] [ OK ]
Connection parameters of [Ensembl Regulation 99] [ OK ]
[NEW CONFIGURATION] .... WITH MEMORY [default]
default ... Ensembl Genes 99 ......... 001/202 ... pcinereus_gene_ensembl .................... (WEB) www.ensembl.org:80 ............
Warning: Too many Options for filter [ chromosome_name ] possible rendering problems for Martview
Use of uninitialized value in lc at biomart-perl/lib/BioMart/Configurator.pm line 469.
OK
default ... Ensembl Genes 99 ......... 002/202 ... atestudineus_gene_ensembl ................. (WEB) www.ensembl.org:80 ............
Use of uninitialized value in lc at biomart-perl/lib/BioMart/Configurator.pm line 469.
.... [omissis] ....
OK
default ... Ensembl Genes 99 ......... 013/202 ... cmilii_gene_ensembl ....................... (WEB) www.ensembl.org:80 ............
Problems with the web server: 500 Internal Server Error
File does not exist: at /biomart-perl/lib/BioMart/Configurator.pm line 170.
Any idea why it seems to download/cache all the 202 species?
To me this seems to happen because the API is not maintained so much anymore?
Anybody managed to get it to work?
Thanks!
Use of uninitialized value in Configurator.pm
When attempting to run any Ensembl generated Perl script, the following warning appears over and over in the output:
Use of uninitialized value in lc at /accre/arch/easybuild/software/Compiler/GCC/5.4.0-2.26/biomart-perl/0.7_e6db561/lib/BioMart/Configurator.pm line 469.
It does not seem to be a critical error since each step completes with OK.
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.