[ensembl-dev] Error Installation Virtual Machine
Tommaso Andreani
andreani.tommaso86 at gmail.com
Tue Mar 12 12:46:34 GMT 2013
Hello,
i follow the step to install API virtual machine but in the final step i've
this error:
./verify-installation: Permission denied
How can i solve this problem? Do i have to follow the API Registry before?
Thanks,
Tommaso
2013/3/12 <dev-request at ensembl.org>
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> Today's Topics:
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> 1. Re: Missense SNP's and frequencies (Will McLaren)
> 2. Transcript coordinates (Jens Christian Nielsen)
> 3. Re: Transcript coordinates (Will McLaren)
>
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Mar 2013 12:00:36 +0000
> From: Will McLaren <wm2 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Missense SNP's and frequencies
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID:
> <CAMVEDX3c_gwQTV7iTVS0nkV7euzABafcM5fZN9VtK-=
> 13v5A6w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jens,
>
> You can use fetch_all_by_Slice_SO_terms to get only variations with a
> particular consequence type, in this case the type you want to limit
> to is "missense_variant":
>
> my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,
> ['missense_variant'])};
>
> To retrieve the global minor allele frequency (this is from the
> combined 1000 genomes phase 1 data), you can use the method
> minor_allele_frequency and minor_allele:
>
> print $vf->minor_allele, ':', $vf->minor_allele_frequency, "\n";
>
> You can get frequencies from many other populations by retrieving the
> allele objects associated with the variation ($vf->get_all_Alleles).
> See the documentation and tutorial pages for more details:
>
> http://www.ensembl.org/info/docs/api/variation/index.html
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
> On 11 March 2013 11:52, Jens Christian Nielsen <jcfnielsen at gmail.com>
> wrote:
> > For a list of genbank accession numbers i wanna extract all missense
> > variations and their frequencies. Right now my script extracts all snp's
> > from the slice ($slice), but how can I restrict it to only print the
> snp's
> > that lead to a change in the protein sequence? Also, i want it to return
> the
> > frequencies of the snp's?
> >
> > use Bio::EnsEMBL::Registry;
> > my $reg = 'Bio::EnsEMBL::Registry';
> > $reg->load_registry_from_db(-host => 'ensembldb.ensembl.org', -user =>
> > 'anonymous');
> > my $gene_name = shift;
> > my $ga = $reg->get_adaptor('Human', 'Core', 'Gene');
> > my $sa = $reg->get_adaptor('Human', 'Core', 'Slice');
> > my $vfa = $reg->get_adaptor('Human', 'Variation', 'VariationFeature');
> >
> > my $genes = $ga->fetch_all_by_external_name($gene_name);
> > while (my $gene = shift @{$genes}) {
> > my $chr = $gene->seq_region_name;
> > my $start = $gene->seq_region_start;
> > my $end = $gene->seq_region_end;
> > my $region = sprintf "%s:%d-%d", $chr, $gene->start, $gene->end;
> > print join("\t", ($gene->stable_id, $region, $length,
> > $gene->external_name, $gene->description) ), "\n";
> > my $slice = $sa->fetch_by_region('chromosome', $chr, $start, $end);
> > my @vfs = @{$vfa->fetch_all_by_Slice($slice)};
> > for my $vf (@vfs) {
> > print
> > $vf->variation_name, ' has alleles ', $vf->allele_string,
> > ' located at ', $slice->seq_region_name, ':',
> > $vf->seq_region_start, '-', $vf->seq_region_end, "\n";
> > }
> > }
> >
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org
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> >
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Mar 2013 16:59:44 +0100
> From: Jens Christian Nielsen <jcfnielsen at gmail.com>
> Subject: [ensembl-dev] Transcript coordinates
> To: dev at ensembl.org
> Message-ID:
> <CAEoXKwHQGuddnko=JwsU=fdY8onnn+1P=-
> KP0MGQGi1vN2USQw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> I am extracting transcripts and missense SNP's from a list of accession
> numbers, but I am having trouble mapping the genome coordinates to the aa
> position in the transcript. Is their a smart way to extract the position of
> the aa mutation counting from the begining of the transcript, so i can
> locate exactly which aa's that are prone to mutations. It seems kind of
> cumbersome to identify positions through the genome coordinates.
>
> This is a piece of my code where i right now am extracting the genome
> coordinates:
>
> my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,
> ['missense_variant'])};
> foreach my $vf (@vfs) {
> my $transcript_variations = $vf->get_all_TranscriptVariations;
>
> if (defined $transcript_variations){
> foreach my $tv (@{$transcript_variations}){
> if (defined $tv->pep_allele_string) { # the AA change
> print $tv->pep_allele_string."\t";
> }
> print $vf->seq_region_name, ":", $vf->start,"-",$vf->end."\n"; # print
> position in Ref in format
> }
> }
> }
> Thanks in advance
>
> Jens
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> ------------------------------
>
> Message: 3
> Date: Mon, 11 Mar 2013 16:10:42 +0000
> From: Will McLaren <wm2 at ebi.ac.uk>
> Subject: Re: [ensembl-dev] Transcript coordinates
> To: Ensembl developers list <dev at ensembl.org>
> Message-ID:
> <
> CAMVEDX1HhKvSc-dOF3MH36O2rPB5qxu-+iwQiYz02ZzcLhhStg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Jens,
>
> The $tv transcript variation objects carry the coordinates in CDS,
> cDNA and protein systems:
>
> print "cdna coords: ", $tv->cdna_start, '-', $tv->cdna_end, "\n";
> print "cds coords: ", $tv->cds_start, '-', $tv->cds_end, "\n";
> print "pep coords: ", $tv->translation_start,
> '-',$tv->translation_end, "\n";
>
> You can also use a transcript mapper to convert between coordinate types:
>
>
> http://www.ensembl.org/info/docs/Doxygen/core-api//classBio_1_1EnsEMBL_1_1TranscriptMapper.html
>
> Regards
>
> Will
>
> On 11 March 2013 15:59, Jens Christian Nielsen <jcfnielsen at gmail.com>
> wrote:
> > I am extracting transcripts and missense SNP's from a list of accession
> > numbers, but I am having trouble mapping the genome coordinates to the aa
> > position in the transcript. Is their a smart way to extract the position
> of
> > the aa mutation counting from the begining of the transcript, so i can
> > locate exactly which aa's that are prone to mutations. It seems kind of
> > cumbersome to identify positions through the genome coordinates.
> >
> > This is a piece of my code where i right now am extracting the genome
> > coordinates:
> >
> > my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,
> > ['missense_variant'])};
> > foreach my $vf (@vfs) {
> > my $transcript_variations = $vf->get_all_TranscriptVariations;
> >
> > if (defined $transcript_variations){
> > foreach my $tv (@{$transcript_variations}){
> > if (defined $tv->pep_allele_string) { # the AA change
> > print $tv->pep_allele_string."\t";
> > }
> > print $vf->seq_region_name, ":", $vf->start,"-",$vf->end."\n"; # print
> > position in Ref in format
> > }
> > }
> > }
> > Thanks in advance
> >
> > Jens
> >
> > _______________________________________________
> > Dev mailing list Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> > http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
> >
>
>
>
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>
> End of Dev Digest, Vol 33, Issue 18
> ***********************************
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