text: user12798: I need to download some of the genomes of human gut microbiome in FASTA format. Anybody has any script to download?
  
  user6628: I'd suggest the bit-dl-ncbi-assemblies from the Bioinformatics Tools package.
  $ bit-dl-ncbi-assemblies
  
   --------------------------------  HELP INFO  --------------------------------- 
  
    This program downloads assembly files for NCBI genomes. It takes as input
    assembly accessions (either GCA_* or GCF_*) and optionally a specification of
    which format to download (currently: genbank, fasta, protein, or gff). For
    version info, run `bit-version`.
  
      Required input:
  
          - [-w <file>] single-column file of NCBI assembly accessions
  
      Optional arguments include:
  
          - [-f <str>] default: genbank
                    Specify the desired format. Available options currently
                    include: genbank, fasta, protein, gff, feature_tab, report, stats.
  
          - [-j <int> ] default: 1
                    The number of downloads you'd like to run in parallel. Write speeds
                    can become problematic generally with around 15 or more, so a max
                    of 12 will be used to be safe even if more are requested.
  
      Example usage:
  
       bit-dl-ncbi-assemblies -w ncbi_accessions.txt -f protein -j 4
  
  Alternatively, you can use this code from the Biopython cookbook:
  import os
  from Bio import SeqIO
  from Bio import Entrez
  
  Entrez.email = "A.N.Other@example.com"  # Always tell NCBI who you are
  
  seq_ids = ["EU490707"] # Your accessions go in this list
  for sid in seq_ids:
      filename = f"{sid}.fasta"
      if not os.path.isfile(filename):
          # Downloading...
          net_handle = Entrez.efetch(
              db="nucleotide", id=sid, rettype="fasta", retmode="text"
          )
          out_handle = open(filename, "w")
          out_handle.write(net_handle.read())
          out_handle.close()
          net_handle.close()
          print("Saved")
  
  
original_text: 12798: <p>I need to download some of the genomes of human gut microbiome in FASTA format. Anybody has any script to download?</p>
   6628: <p>I'd suggest the <code>bit-dl-ncbi-assemblies</code> from the <a href="https://github.com/AstrobioMike/bit" rel="nofollow noreferrer">Bioinformatics Tools</a> package.</p>
  <pre><code>$ bit-dl-ncbi-assemblies
  
   --------------------------------  HELP INFO  --------------------------------- 
  
    This program downloads assembly files for NCBI genomes. It takes as input
    assembly accessions (either GCA_* or GCF_*) and optionally a specification of
    which format to download (currently: genbank, fasta, protein, or gff). For
    version info, run `bit-version`.
  
      Required input:
  
          - [-w &lt;file&gt;] single-column file of NCBI assembly accessions
  
      Optional arguments include:
  
          - [-f &lt;str&gt;] default: genbank
                    Specify the desired format. Available options currently
                    include: genbank, fasta, protein, gff, feature_tab, report, stats.
  
          - [-j &lt;int&gt; ] default: 1
                    The number of downloads you'd like to run in parallel. Write speeds
                    can become problematic generally with around 15 or more, so a max
                    of 12 will be used to be safe even if more are requested.
  
      Example usage:
  
       bit-dl-ncbi-assemblies -w ncbi_accessions.txt -f protein -j 4
  </code></pre>
  <p>Alternatively, you can use this code from the <a href="http://biopython.org/DIST/docs/tutorial/Tutorial.html#sec149" rel="nofollow noreferrer">Biopython cookbook</a>:</p>
  <pre class="lang-py prettyprint-override"><code>import os
  from Bio import SeqIO
  from Bio import Entrez
  
  Entrez.email = &quot;A.N.Other@example.com&quot;  # Always tell NCBI who you are
  
  seq_ids = [&quot;EU490707&quot;] # Your accessions go in this list
  for sid in seq_ids:
      filename = f&quot;{sid}.fasta&quot;
      if not os.path.isfile(filename):
          # Downloading...
          net_handle = Entrez.efetch(
              db=&quot;nucleotide&quot;, id=sid, rettype=&quot;fasta&quot;, retmode=&quot;text&quot;
          )
          out_handle = open(filename, &quot;w&quot;)
          out_handle.write(net_handle.read())
          out_handle.close()
          net_handle.close()
          print(&quot;Saved&quot;)
  </code></pre>
  