<div dir="ltr">Hi Sabrina,<div><br></div><div>There is indeed a way, though it requires a little knowledge of the internals of the VEP to get it working.</div><div><br></div><div>To retrieve the data off disk is simple enough, but some method calls you can normally make on a transcript object (e.g. translateable_seq() to get the CDS sequence) won't work. Best thing to do is to step in with the perl debugger and explore the contents of the $tr object.</div><div><br></div><div>Here's a script to retrieve the transcripts in a given 1MB region and dump out the CDS sequences as FASTA. You'll need to modify the $config hash to point to your particular directory, and the region specifics will need changing according to which you want to dump.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div><div><font face="monospace, monospace">###</font></div><div><font face="monospace, monospace">### BEGIN SCRIPT</font></div><div><span style="font-family:monospace,monospace">###</span></div><div><span style="font-family:monospace,monospace">use Bio::EnsEMBL::Variation::Utils::VEP qw(load_dumped_transcript_cache);</span></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"># config hash defines a few things needed for method to work</font></div><div><font face="monospace, monospace">my $config = {</font></div><div><font face="monospace, monospace"> 'compress' => 'gzip -dc', # required; try 'zcat' instead if this doesn't work</font></div><div><font face="monospace, monospace"> 'dir' => '/Users/will/.vep/homo_sapiens/80_GRCh38', # full path to VEP cache including species, version, assembly</font></div><div><font face="monospace, monospace"> 'quiet' => 1, # not required but stops splurge</font></div><div><font face="monospace, monospace">};</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"># define region</font></div><div><font face="monospace, monospace"># regions in the cache are of fixed size (1MB) with one cache file per MB</font></div><div><font face="monospace, monospace"># files are named after these region names under chromosome sub-directories</font></div><div><font face="monospace, monospace"># in the VEP cache directory, so it's easy to loop over them if you read</font></div><div><font face="monospace, monospace"># the contents of the directory</font></div><div><font face="monospace, monospace">my $chr = 1;</font></div><div><font face="monospace, monospace">my $region_start = 1000001; # region start must be (r * 10^6) + 1</font></div><div><font face="monospace, monospace">my $region_end = 2000000; # region end must be (r + 1) * 10^6</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace"># this returns a hashref with one member keyed on chromosome name</font></div><div><font face="monospace, monospace">my $trs = load_dumped_transcript_cache($config, $chr, $region_start.'-'.$region_end);</font></div><div><font face="monospace, monospace"><br></font></div><div><font face="monospace, monospace">foreach my $tr(@{$trs->{$chr}}) {</font></div><div><font face="monospace, monospace"> printf(</font></div><div><font face="monospace, monospace"> ">%s\n%s\n",</font></div><div><font face="monospace, monospace"> $tr->stable_id, # some methods can be called verbatim</font></div><div><font face="monospace, monospace"> $tr->{_variation_effect_feature_cache}->{translateable_seq} # others use internal cache</font></div><div><font face="monospace, monospace"> );</font></div><div><font face="monospace, monospace">}</font></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 31 August 2015 at 08:44, Sabrina Legoueix Rodriguez <span dir="ltr"><<a href="mailto:sabrina.rodriguez@toulouse.inra.fr" target="_blank">sabrina.rodriguez@toulouse.inra.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Dear all,<br>
<div> <br>
I am working on a specie whose reference genome is not publicly
available. I have a .gtf file for CDS annotations and a fasta file
for the genome sequence.<br>
<br>
I am using <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a> to generate my .vep file from my .vcf file.<br>
<br>
I would like to obtain the transcript nucleotide sequences of my
CDSs ( coding sequences of my genes without UTRs...).<br>
Is there a way to connect to the cache file generated with
<a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a> (instead of the database registry) and use Ensembl API
objects to get the coding sequences of my genes?<br>
<br>
Thanks in advance for your answer.<br>
<br>
Best regards,<br>
<br>
<div>-- <br>
<br>
Sabrina <br>
<br>
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