text: user2876: I am trying to use bedtools and fetch sequences from a whole genome fasta file inside the script I get region coordinates as variables.
  For example:
  chr_ = "chr1"
  start = 3000
  end = 3402
  
  I am not sure how to wrap my function, because the example provided by BedTool.sequence only uses coordinates in a string form.
  Can you please help me to have something like this?
  a = pybedtools.BedTool(chr_, start, end, from_variables=True)
  
  
  user964: You have to take your variables and make them into a single string variable.
  for example:
  chr_ = "chr1"
  start = 3000
  end = 3402
  as_str = ' '.join([chr_, str(start), str(end)])
  # or 
  as_str2 = "{} {} {}".format(chr_, start, end)
  
  Once you have the string built you can use the example in the bedTool docs.
  a = BedTool(as_str, from_string=True)
  
  
original_text: 2876: <p>I am trying to use bedtools and fetch sequences from a whole genome fasta file inside the script I get region coordinates as variables.
  For example:</p>
  
  <pre><code>chr_ = "chr1"
  start = 3000
  end = 3402
  </code></pre>
  
  <p>I am not sure how to wrap my function, because the example provided by <a href="https://daler.github.io/pybedtools/autodocs/pybedtools.bedtool.BedTool.sequence.html#pybedtools.bedtool.BedTool.sequence" rel="nofollow noreferrer">BedTool.sequence</a> only uses coordinates in a string form.</p>
  
  <p>Can you please help me to have something like this?</p>
  
  <pre><code>a = pybedtools.BedTool(chr_, start, end, from_variables=True)
  </code></pre>
   964: <p>You have to take your variables and make them into a single string variable.</p>
  
  <p>for example:</p>
  
  <pre><code>chr_ = "chr1"
  start = 3000
  end = 3402
  as_str = ' '.join([chr_, str(start), str(end)])
  # or 
  as_str2 = "{} {} {}".format(chr_, start, end)
  </code></pre>
  
  <p>Once you have the string built you can use the example in the <a href="https://daler.github.io/pybedtools/autodocs/pybedtools.bedtool.BedTool.html" rel="nofollow noreferrer">bedTool docs</a>.</p>
  
  <pre><code>a = BedTool(as_str, from_string=True)
  </code></pre>
  