<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">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"><u></u>

  
    
  
  <div>
    <p><i></i> </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">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">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">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">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">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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