[ensembl-dev] Error Installation Virtual Machine
Andy Yates
ayates at ebi.ac.uk
Wed Mar 13 08:23:45 GMT 2013
Hi
Yes the script went into cvs without the execution bit set. We've got systems to manually change this so the error will go in our next release.
Andy
Sent from my mobile.
On 12 Mar 2013, at 13:30, Michael Gray <mg13 at sanger.ac.uk> wrote:
> Ah, I encountered this when I installed the Virtual Machine a couple of weeks ago, and then forgot to report it. I think it's a permissions problem.
>
> Try:
>
> chmod +x ./verify-installation
> ./verify-installation
>
> --
> Michael
>
>
> On 12 Mar 2013, at 12:46, Tommaso Andreani wrote:
>
>> 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:
>>>
>>> 1. Re: Missense SNP's and frequencies (Will McLaren)
>>> 2. Transcript coordinates (Jens Christian Nielsen)
>>> 3. Re: Transcript coordinates (Will McLaren)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> 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, '-', $vf->seq_region_end, "\n";
>>> > }
>>> > }
>>> >
>>> > _______________________________________________
>>> > Dev mailing list Dev at ensembl.org
>>> > Posting guidelines and subscribe/unsubscribe info:
>>> > http://lists.ensembl.org/mailman/listinfo/dev
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>>> >
>>>
>>>
>>>
>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Mon, 11 Mar 2013 16:59:44 +0100
>>> From: Jens Christian Nielsen <jcfnielsen at gmail.com>
>>> Subject: [ensembl-dev] Transcript coordinates
>>> To: dev at ensembl.org
>>> Message-ID:
>>> <CAEoXKwHQGuddnko=JwsU=fdY8onnn+1P=-KP0MGQGi1vN2USQw at mail.gmail.com>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> I am extracting transcripts and missense SNP's from a list of accession
>>> numbers, but I am having trouble mapping the genome coordinates to the aa
>>> position in the transcript. Is their a smart way to extract the position of
>>> the aa mutation counting from the begining of the transcript, so i can
>>> locate exactly which aa's that are prone to mutations. It seems kind of
>>> cumbersome to identify positions through the genome coordinates.
>>>
>>> This is a piece of my code where i right now am extracting the genome
>>> coordinates:
>>>
>>> my @vfs = @{$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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