text: user16429: I am having possibly a simple question which is proving difficult.
  My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly pattern I would say).
  
  I first want to see that how many times each enzyme cut the FASTA file and;
  second to check the number and size of fragment that each enzyme would give me, this output pregerably would be a CSV file may be.
  
  Background I tried to do pattern search using R, but its just collapsing my system. I am looking for bash command may be.
  
  user3818: Biopython has a module dedicated to working with restriction enzymes. Without any code examples we cannot help you much further.
  
  user7307: The diffHic package might have solved this issue in R.
  # Load the genomic data
  genome <- biostrings::readDNAStringSet("your_file.fa")
  
  # Run the in silico restriction digest 
  cuts <- cutGenome(genome, "CCGCGG", overhang=2L) # SacII
  
  the cuts GRanges object contains the boundaries of each restriction fragment for given genome.
  
original_text: 16429: <p>I am having possibly a simple question which is proving difficult.</p>
  <p>My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly pattern I would say).</p>
  <ol>
  <li>I first want to see that how many times each enzyme cut the FASTA file and;</li>
  <li>second to check the number and size of fragment that each enzyme would give me, this output pregerably would be a CSV file may be.</li>
  </ol>
  <p><strong>Background</strong> I tried to do pattern search using R, but its just collapsing my system. I am looking for bash command may be.</p>
   3818: <p>Biopython has a module dedicated to working with <a href="http://biopython.org/DIST/docs/cookbook/Restriction.html" rel="nofollow noreferrer">restriction enzymes</a>. Without any code examples we cannot help you much further.</p>
   7307: <p>The <code>diffHic</code> package might have solved this issue in R.</p>
  <pre><code># Load the genomic data
  genome &lt;- biostrings::readDNAStringSet(&quot;your_file.fa&quot;)
  
  # Run the in silico restriction digest 
  cuts &lt;- cutGenome(genome, &quot;CCGCGG&quot;, overhang=2L) # SacII
  </code></pre>
  <p>the <code>cuts</code> GRanges object contains the boundaries of each restriction fragment for given genome.</p>
  