text: user16493: Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here.
  However, I do not see any way to directly wget the gff from this page. What I can do is click "Send to" at the top, select File, and change the Format dropdown to GFF3, and finally click 'Create File', and the gff file downloads onto my computer.
  But then I lose the ability to use the -a flag to log the download details, I can't download the gff using wget from a remote server directly but instead I need to download it locally and then upload it, etc. Is there any way to use wget to download gff files from NCBI programmatically instead of having to download it manually from the website?
  
  user16493: I believe I figured out a way to do this for my particular example (although in general cases Adrian's answer works). To get release 5.57 (an earlier release) of chromosome X of Drosophila melanogaster, I believe you can go to the Datasets Genome page of D. melanogaster, scroll down to the Revision History and select Release 5, and at the top of the page, NCBI lets you click on a 'datasets' or 'curl' box to copy the exact command line argument needed to download a GFF (and other files) of that whole genome. Then, I believe it should be possible to open the gff in Python using a package like gffutils, and filter only for chromosome X rows, and then write those rows to a new gff file.
  
  user16386: my suggestion would be to go via the assembly page.
  For your example link, I would
  
  Click the link to the BioProject: PRJNA164
  On the right side, under "Related information" choose the assembly
  On the assembly page, under "Access the data" on the right side, I would choose "FTP directory for RefSeq assembly"
  
  Once in the RefSeq folder, copy the link to the *_genomic.gff.gz and use wget.
  wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.gff.gz
  
  
  Edit: The initial question requested an older versions, which can be found in RefSeq's archive of prior releases. For this specific Drosophila assembly chromosome X, the version 5 can be found at https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Drosophila_melanogaster/RELEASE_5/CHR_X/NC_004354.gff
  
original_text: 16493: <p>Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_004354.3" rel="nofollow noreferrer">is here</a>.</p>
  <p>However, I do not see any way to directly wget the gff from this page. What I can do is click &quot;Send to&quot; at the top, select File, and change the Format dropdown to GFF3, and finally click 'Create File', and the gff file downloads onto my computer.</p>
  <p>But then I lose the ability to use the -a flag to log the download details, I can't download the gff using wget from a remote server directly but instead I need to download it locally and then upload it, etc. Is there any way to use wget to download gff files from NCBI programmatically instead of having to download it manually from the website?</p>
   16493: <p>I believe I figured out a way to do this for my particular example (although in general cases Adrian's answer works). To get release 5.57 (an earlier release) of chromosome X of Drosophila melanogaster, I believe you can go to the <a href="https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000001215.4/" rel="nofollow noreferrer">Datasets Genome page</a> of D. melanogaster, scroll down to the Revision History and select Release 5, and at the top of the page, NCBI lets you click on a 'datasets' or 'curl' box to copy the exact command line argument needed to download a GFF (and other files) of that whole genome. Then, I believe it should be possible to open the gff in Python using a package like gffutils, and filter only for chromosome X rows, and then write those rows to a new gff file.</p>
   16386: <p>my suggestion would be to go via the assembly page.
  For your example link, I would</p>
  <ol>
  <li>Click the link to the BioProject: PRJNA164</li>
  <li>On the right side, under &quot;Related information&quot; choose the <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.4" rel="nofollow noreferrer">assembly</a></li>
  <li>On the assembly page, under &quot;Access the data&quot; on the right side, I would choose &quot;FTP directory for RefSeq assembly&quot;</li>
  </ol>
  <p>Once in the RefSeq folder, copy the link to the <code>*_genomic.gff.gz</code> and use wget.</p>
  <pre><code>wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/215/GCF_000001215.4_Release_6_plus_ISO1_MT/GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.gff.gz
  </code></pre>
  <hr />
  <p><strong>Edit</strong>: The initial question requested an older versions, which can be found in RefSeq's <a href="https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/" rel="nofollow noreferrer">archive</a> of prior releases. For this specific Drosophila assembly chromosome X, the version 5 can be found at <a href="https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Drosophila_melanogaster/RELEASE_5/CHR_X/NC_004354.gff" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Drosophila_melanogaster/RELEASE_5/CHR_X/NC_004354.gff</a></p>
  