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<p>Dear Allan,</p>
<p>Thanks for your message, and happy to help.</p>
<p>As per your last question, I am not aware of a file describing
the entire directory tree TBH.<br>
It is possibly something for us to consider providing.</p>
<p>This said, the directory tree for FASTA is similar to the GFF3
one</p>
<p>For plants<br>
<a class="moz-txt-link-freetext" href="http://ftp.ensemblgenomes.org/pub/plants/release-60/fasta/">http://ftp.ensemblgenomes.org/pub/plants/release-60/fasta/</a><species>/[cdna,cds,dna,dna_index,ncrna,pep]</p>
<p>For bacteria<br>
<a class="moz-txt-link-freetext" href="http://ftp.ensemblgenomes.org/pub/bacteria/release-60/fasta/">http://ftp.ensemblgenomes.org/pub/bacteria/release-60/fasta/</a><collection>/<species>/[cdna,cds,dna,dna_index,ncrna,pep]</p>
<p>The extra complexity layer here is because of the type of
sequence you may be interested in; please, see the options in the
square brackets above.</p>
<p>Regrettably, there is no explicit (and convenient) mapping
assembly accession --> fasta: for the time being you have to
create it using the species metadata file(s).</p>
<p>accession --> (collection,)species --> fasta files</p>
<p>Hope it helps</p>
<p>Kind regards,</p>
<p>Stefano</p>
<div class="moz-cite-prefix">On 11/07/2025 2:42 pm, Allan Kamau
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAF3N6oQfDGCKww4YCz39V7EcdDH+5=9vAvA_PCRcq4_ETYwrrQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Dear Stefano,
<div><br>
</div>
<div>Thank you for your reply and advice.</div>
<div><br>
</div>
<div>I am now constructing the ftp urls to gtf resources using
data from the species field and data extracted from core_db
field as you suggested.</div>
<div><br>
</div>
<div>Regarding fasta data, is there metadata containing the
entire directory tree of the entire ftp directory by which I
could easily identify the specific fasta file type for a given
accession?</div>
<div><br>
</div>
<div>Regards,</div>
<div>Allan.</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Jul 10, 2025 at
1:58 PM Stefano Giorgetti <<a
href="mailto:sgiorgetti@ebi.ac.uk" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">sgiorgetti@ebi.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote"
style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p> </p>
<p>Dear Allan,</p>
<p>Thanks for your email and for using Ensembl services.<br>
</p>
<p>We have 2 main cases: stand-alone species (for instance
all the plants') and species sharing a "collection DB" -
like bacteria.</p>
<p>For the stand-alone species - say plants - the path to
the (release 60) GTF would be<br>
<a
href="http://ftp.ensemblgenomes.org/pub/plants/release-60/gtf/"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">http://ftp.ensemblgenomes.org/pub/plants/release-60/gtf/</a><species>/<br>
where <species> can be found from one of the species
metadata files.</p>
<div>For species belonging to a collection - say bacteria -
the path to the (release 60) GTF would be<br>
<a
href="http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/</a><collection>/<species>/<br>
Regrettably, there is no trivial way to get the collection
the species belongs to.<br>
One hopefully not-too-cumbersome would be to extract it
from the "core_db" field from the species metadata file.<br>
For instance for "acetobacter_syzygii_gca_002276805", we
have core db "bacteria_60_collection_core_60_113_1", the
collection name would be "bacteria_60_collection"; thus
giving <a
href="http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_60_collection/acetobacter_syzygii_gca_002276805/"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">http://ftp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_60_collection/acetobacter_syzygii_gca_002276805/</a><i><br>
</i></div>
<div><i><br>
</i></div>
<div>Hope it helps.<br>
Any questions, please do not hesitate to ask.<br>
</div>
<div><br>
</div>
<div>Kind regards,</div>
<div>Stefano on behalf of the Ensembl team<i><br>
</i></div>
<div><i><br>
</i></div>
<div>On 10/07/2025 6:49 am, Allan Kamau wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">Greetings,
<div><br>
</div>
<div>Given an entry from one of the species metadata
files such as "<a
href="http://ftp.ensemblgenomes.org/pub/plants/release-60/species_EnsemblPlants.txt"
target="_blank" moz-do-not-send="true">ftp.ensemblgenomes.org/pub/plants/release-60/species_EnsemblPlants.txt</a>"
I would like to determine the ftp path to the "gtf"
data of the given species.
<div><br>
</div>
<div>Is there such a mapping file or mechanism that
I can use?</div>
<div><br>
</div>
<div>Or in short if I have an "assembly" value such
as "ASM16007v2" or and an "assembly_accession"
label for example "GCA_000160075.2" is there a way
to determine the ftp path to the gtf data which is
"<a
href="http://tp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_118_collection/abiotrophia_defectiva_atcc_49176_gca_000160075"
target="_blank" moz-do-not-send="true">tp.ensemblgenomes.org/pub/release-60/bacteria/gtf/bacteria_118_collection/abiotrophia_defectiva_atcc_49176_gca_000160075</a>"
in this case?</div>
<div><br>
</div>
<div>Regards,</div>
<div>- Allan.</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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