text: user274: Dear bioinformaticians,
  I could find two python APIs to mine ENSEMBL genome databases. There is a pyensembl which is more popular and then there is genomepy which is less popular. Following is my experience with both.
  1. pyensembl:
  pyensembl is a fast and powerful API to mine ENSEMBL genome databases. 
  I have been using it for a while and in my experience it works very well. The name of the package may make you believe that it is developed/maintained by ENSEMBL. That is not true. Still, being an open source package with a realistic potential to be the default API for mining ENSEMBL genome databases.
  However, there are some issues related to it's development that users may find disconcerting.
  For example, documentation. I could only find a comprehensive api documentation for release 0.8.10. Current release is 1.1. Not even release notes are available. Therefore users have to rely on few lines of documentation that is available in the README.md. 
  Also, as far as I know, it is not peer reviewed even though it is an excellent analysis resource.
  2. genomepy
  genomepy loads all of the genome files into the RAM, making it immediately unusable, especially if you are working with larger genome such as human genome.
  So my question is: Is there any other better python API for working with ENSEMBL genomes?
  
  user1332: The correct API for Ensembl is the Ensembl REST API which is updated and maintained by Ensembl, and language agnostic.
  
  user4824: Now there's another option, the ensembl_rest module, a thin wrapper around the Ensembl REST API to simplify its usage and make it more pythonic. You can find the documentation here. 
  To clarify things, I'm the creator and maintainer, but still think it's a legitimate alternative.
  
original_text: 274: <p>Dear bioinformaticians,</p>
  
  <p>I could find two python APIs to mine ENSEMBL genome databases. There is a <a href="https://github.com/openvax/pyensembl" rel="nofollow noreferrer"><code>pyensembl</code></a> which is more popular and then there is <a href="https://github.com/simonvh/genomepy" rel="nofollow noreferrer"><code>genomepy</code></a> which is less popular. Following is my experience with both.</p>
  
  <p><strong>1. <code>pyensembl</code>:</strong></p>
  
  <p><code>pyensembl</code> is a fast and powerful API to mine ENSEMBL genome databases. 
  I have been using it for a while and in my experience it works very well. The name of the package may make you believe that it is developed/maintained by ENSEMBL. That is not true. Still, being an open source package with a realistic potential to be the default API for mining ENSEMBL genome databases.</p>
  
  <p>However, there are some issues related to it's development that users may find disconcerting.</p>
  
  <p>For example, documentation. I could only find a comprehensive api <a href="https://media.readthedocs.org/pdf/pyensembl/latest/pyensembl.pdf" rel="nofollow noreferrer">documentation for release 0.8.10</a>. Current release is 1.1. Not even <a href="https://github.com/openvax/pyensembl/releases" rel="nofollow noreferrer">release notes are available</a>. Therefore users have to rely on few lines of documentation that is available in the <a href="https://github.com/openvax/pyensembl/blob/master/README.md" rel="nofollow noreferrer">README.md</a>. </p>
  
  <p>Also, as far as I know, it is not peer reviewed even though it is an excellent analysis resource.</p>
  
  <p><strong>2. <code>genomepy</code></strong></p>
  
  <p><code>genomepy</code> loads all of the genome files into the RAM, making it immediately unusable, especially if you are working with larger genome such as human genome.</p>
  
  <p>So my question is: Is there any other better python API for working with ENSEMBL genomes?</p>
   1332: <p>The correct API for Ensembl is the <a href="http://rest.ensembl.org/documentation" rel="nofollow noreferrer">Ensembl REST API</a> which is updated and maintained by Ensembl, and language agnostic.</p>
   4824: <p>Now there's another option, the <code>ensembl_rest</code> module, a thin wrapper around the <a href="http://rest.ensembl.org" rel="noreferrer">Ensembl REST API</a> to simplify its usage and make it more pythonic. You can find the documentation <a href="https://ensemblrest.readthedocs.io" rel="noreferrer">here</a>. </p>
  
  <p>To clarify things, I'm the creator and maintainer, but still think it's a legitimate alternative.</p>
  