<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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.<div><br></div><div>Try:</div><div><br></div><div> chmod +x ./verify-installation</div><div> ./verify-installation</div><div><br></div><div>-- </div><div>Michael</div><div><br></div><div><br><div><div>On 12 Mar 2013, at 12:46, Tommaso Andreani wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,</div><div>i follow the step to install API virtual machine but in the final step i've this error:</div><div>./verify-installation: Permission denied</div><div><br></div><div>How can i solve this problem? Do i have to follow the API Registry before?</div>
<div>Thanks,</div><div>Tommaso</div><div><br></div><br><div class="gmail_quote">2013/3/12 <span dir="ltr"><<a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
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1. Re: Missense SNP's and frequencies (Will McLaren)<br>
2. Transcript coordinates (Jens Christian Nielsen)<br>
3. Re: Transcript coordinates (Will McLaren)<br>
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<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 11 Mar 2013 12:00:36 +0000<br>
From: Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] Missense SNP's and frequencies<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID:<br>
<CAMVEDX3c_gwQTV7iTVS0nkV7euzABafcM5fZN9VtK-=<a href="mailto:13v5A6w@mail.gmail.com">13v5A6w@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi Jens,<br>
<br>
You can use fetch_all_by_Slice_SO_terms to get only variations with a<br>
particular consequence type, in this case the type you want to limit<br>
to is "missense_variant":<br>
<br>
my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice, ['missense_variant'])};<br>
<br>
To retrieve the global minor allele frequency (this is from the<br>
combined 1000 genomes phase 1 data), you can use the method<br>
minor_allele_frequency and minor_allele:<br>
<br>
print $vf->minor_allele, ':', $vf->minor_allele_frequency, "\n";<br>
<br>
You can get frequencies from many other populations by retrieving the<br>
allele objects associated with the variation ($vf->get_all_Alleles).<br>
See the documentation and tutorial pages for more details:<br>
<br>
<a href="http://www.ensembl.org/info/docs/api/variation/index.html" target="_blank">http://www.ensembl.org/info/docs/api/variation/index.html</a><br>
<br>
Regards<br>
<br>
Will McLaren<br>
Ensembl Variation<br>
<br>
On 11 March 2013 11:52, Jens Christian Nielsen <<a href="mailto:jcfnielsen@gmail.com">jcfnielsen@gmail.com</a>> wrote:<br>
> For a list of genbank accession numbers i wanna extract all missense<br>
> variations and their frequencies. Right now my script extracts all snp's<br>
> from the slice ($slice), but how can I restrict it to only print the snp's<br>
> that lead to a change in the protein sequence? Also, i want it to return the<br>
> frequencies of the snp's?<br>
><br>
> use Bio::EnsEMBL::Registry;<br>
> my $reg = 'Bio::EnsEMBL::Registry';<br>
> $reg->load_registry_from_db(-host => '<a href="http://ensembldb.ensembl.org/" target="_blank">ensembldb.ensembl.org</a>', -user =><br>
> 'anonymous');<br>
> my $gene_name = shift;<br>
> my $ga = $reg->get_adaptor('Human', 'Core', 'Gene');<br>
> my $sa = $reg->get_adaptor('Human', 'Core', 'Slice');<br>
> my $vfa = $reg->get_adaptor('Human', 'Variation', 'VariationFeature');<br>
><br>
> my $genes = $ga->fetch_all_by_external_name($gene_name);<br>
> while (my $gene = shift @{$genes}) {<br>
> my $chr = $gene->seq_region_name;<br>
> my $start = $gene->seq_region_start;<br>
> my $end = $gene->seq_region_end;<br>
> my $region = sprintf "%s:%d-%d", $chr, $gene->start, $gene->end;<br>
> print join("\t", ($gene->stable_id, $region, $length,<br>
> $gene->external_name, $gene->description) ), "\n";<br>
> my $slice = $sa->fetch_by_region('chromosome', $chr, $start, $end);<br>
> my @vfs = @{$vfa->fetch_all_by_Slice($slice)};<br>
> for my $vf (@vfs) {<br>
> print<br>
> $vf->variation_name, ' has alleles ', $vf->allele_string,<br>
> ' located at ', $slice->seq_region_name, ':',<br>
> $vf->seq_region_start, '-', $vf->seq_region_end, "\n";<br>
> }<br>
> }<br>
><br>
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><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 11 Mar 2013 16:59:44 +0100<br>
From: Jens Christian Nielsen <<a href="mailto:jcfnielsen@gmail.com">jcfnielsen@gmail.com</a>><br>
Subject: [ensembl-dev] Transcript coordinates<br>
To: <a href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Message-ID:<br>
<CAEoXKwHQGuddnko=JwsU=fdY8onnn+1P=-<a href="mailto:KP0MGQGi1vN2USQw@mail.gmail.com">KP0MGQGi1vN2USQw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
I am extracting transcripts and missense SNP's from a list of accession<br>
numbers, but I am having trouble mapping the genome coordinates to the aa<br>
position in the transcript. Is their a smart way to extract the position of<br>
the aa mutation counting from the begining of the transcript, so i can<br>
locate exactly which aa's that are prone to mutations. It seems kind of<br>
cumbersome to identify positions through the genome coordinates.<br>
<br>
This is a piece of my code where i right now am extracting the genome<br>
coordinates:<br>
<br>
my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,<br>
['missense_variant'])};<br>
foreach my $vf (@vfs) {<br>
my $transcript_variations = $vf->get_all_TranscriptVariations;<br>
<br>
if (defined $transcript_variations){<br>
foreach my $tv (@{$transcript_variations}){<br>
if (defined $tv->pep_allele_string) { # the AA change<br>
print $tv->pep_allele_string."\t";<br>
}<br>
print $vf->seq_region_name, ":", $vf->start,"-",$vf->end."\n"; # print<br>
position in Ref in format<br>
}<br>
}<br>
}<br>
Thanks in advance<br>
<br>
Jens<br>
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<br>
Message: 3<br>
Date: Mon, 11 Mar 2013 16:10:42 +0000<br>
From: Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
Subject: Re: [ensembl-dev] Transcript coordinates<br>
To: Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
Message-ID:<br>
<<a href="mailto:CAMVEDX1HhKvSc-dOF3MH36O2rPB5qxu-%2BiwQiYz02ZzcLhhStg@mail.gmail.com">CAMVEDX1HhKvSc-dOF3MH36O2rPB5qxu-+iwQiYz02ZzcLhhStg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br>
<br>
Hi Jens,<br>
<br>
The $tv transcript variation objects carry the coordinates in CDS,<br>
cDNA and protein systems:<br>
<br>
print "cdna coords: ", $tv->cdna_start, '-', $tv->cdna_end, "\n";<br>
print "cds coords: ", $tv->cds_start, '-', $tv->cds_end, "\n";<br>
print "pep coords: ", $tv->translation_start,<br>
'-',$tv->translation_end, "\n";<br>
<br>
You can also use a transcript mapper to convert between coordinate types:<br>
<br>
<a href="http://www.ensembl.org/info/docs/Doxygen/core-api//classBio_1_1EnsEMBL_1_1TranscriptMapper.html" target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api//classBio_1_1EnsEMBL_1_1TranscriptMapper.html</a><br>
<br>
Regards<br>
<br>
Will<br>
<br>
On 11 March 2013 15:59, Jens Christian Nielsen <<a href="mailto:jcfnielsen@gmail.com">jcfnielsen@gmail.com</a>> wrote:<br>
> I am extracting transcripts and missense SNP's from a list of accession<br>
> numbers, but I am having trouble mapping the genome coordinates to the aa<br>
> position in the transcript. Is their a smart way to extract the position of<br>
> the aa mutation counting from the begining of the transcript, so i can<br>
> locate exactly which aa's that are prone to mutations. It seems kind of<br>
> cumbersome to identify positions through the genome coordinates.<br>
><br>
> This is a piece of my code where i right now am extracting the genome<br>
> coordinates:<br>
><br>
> my @vfs = @{$vfa-> fetch_all_by_Slice_SO_terms($slice,<br>
> ['missense_variant'])};<br>
> foreach my $vf (@vfs) {<br>
> my $transcript_variations = $vf->get_all_TranscriptVariations;<br>
><br>
> if (defined $transcript_variations){<br>
> foreach my $tv (@{$transcript_variations}){<br>
> if (defined $tv->pep_allele_string) { # the AA change<br>
> print $tv->pep_allele_string."\t";<br>
> }<br>
> print $vf->seq_region_name, ":", $vf->start,"-",$vf->end."\n"; # print<br>
> position in Ref in format<br>
> }<br>
> }<br>
> }<br>
> Thanks in advance<br>
><br>
> Jens<br>
><br>
> _______________________________________________<br>
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><br>
<br>
<br>
<br>
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End of Dev Digest, Vol 33, Issue 18<br>
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</blockquote></div><br>
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