text: user6738: I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/ which can perform this task, but my files (bacterial genomes) are too big.
  Can anyone suggest a simple method to make this conversion?
  
  user3233: You can use BioPerl to do this. Read in the GFF and make gene objects and write out those gene objects in Genbank format.
  Perhaps this tool (doing the opposite) will get you started:
  https://metacpan.org/pod/bp_genbank2gff3.pl
  Here is a script doing what you ask but it doesn't use any libraries (so is probably buggy):
  https://gist.github.com/avrilcoghlan/5386810
  Hope that helps,
  Dan.
  
  user123: Here's a python script based on the bcbio-gff (reading gff3) and biopython (writing genbank): https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py
  
  user6767: I believe seqret is already the simplest approach. If you install the emboss command line utility, genome (file) sizes will not be a problem. You can even install it with conda, see https://anaconda.org/bioconda/emboss.
  After that, you can use it as the example:
  seqret -sequence {genome file} -feature -fformat gff -fopenfile {gff file} -osformat genbank -osname_outseq {output prefix} -ofdirectory_outseq gbk_file -auto
  
  Hope it helps
  
original_text: 6738: <p>I want to convert my gff3 annotation files to genbank format for use in Mauve. I found the seqret tool here <a href="https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/" rel="nofollow noreferrer">https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/</a> which can perform this task, but my files (bacterial genomes) are too big.</p>
  
  <p>Can anyone suggest a simple method to make this conversion?</p>
   3233: <p>You can use BioPerl to do this. Read in the GFF and make gene objects and write out those gene objects in Genbank format.</p>
  
  <p>Perhaps this tool (doing the opposite) will get you started:
  <a href="https://metacpan.org/pod/bp_genbank2gff3.pl" rel="nofollow noreferrer">https://metacpan.org/pod/bp_genbank2gff3.pl</a></p>
  
  <p>Here is a script doing what you ask but it doesn't use any libraries (so is probably buggy):
  <a href="https://gist.github.com/avrilcoghlan/5386810" rel="nofollow noreferrer">https://gist.github.com/avrilcoghlan/5386810</a></p>
  
  <p>Hope that helps,
  Dan.</p>
   123: <p>Here's a python script based on the <a href="https://github.com/chapmanb/bcbb/tree/master/gff" rel="nofollow noreferrer">bcbio-gff</a> (reading gff3) and <a href="https://biopython.org/" rel="nofollow noreferrer">biopython</a> (writing genbank): <a href="https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py" rel="nofollow noreferrer">https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py</a></p>
   6767: <p>I believe <code>seqret</code> is already the simplest approach. If you install the emboss command line utility, genome (file) sizes will not be a problem. You can even install it with conda, see <a href="https://anaconda.org/bioconda/emboss" rel="nofollow noreferrer">https://anaconda.org/bioconda/emboss</a>.</p>
  
  <p>After that, you can use it as the example:</p>
  
  <pre><code>seqret -sequence {genome file} -feature -fformat gff -fopenfile {gff file} -osformat genbank -osname_outseq {output prefix} -ofdirectory_outseq gbk_file -auto
  </code></pre>
  
  <p>Hope it helps</p>
  