Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-14T17:07:14.633Z
Answers.LastActivityDate: 2020-01-14T17:07:14.633Z
Answers.UserDisplayName: Felipe Almeida
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-13T13:55:52.120Z
Answers.LastActivityDate: 2020-01-13T13:55:52.120Z
Answers.UserDisplayName: Dan Bolser
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-02-07T23:36:23.453Z
Answers.Text: just random ref, can `pip install bcbio-gff` and `pip install BioPython` to get these dependencies for this
Answers.UserDisplayName: Colin D
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Answers.CreationDate: 2022-07-16T11:23:30.180Z
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Answers.UserDisplayName: mgalardini
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-09T16:56:57.173Z
Comments.Text: Hi there. I don't know any simple method for what you ask, mainly because `gff3` format does not contain sequences (only annotations) while `fasta` & `genbank` do. This thread on biostars might help tho :  [Gff3 + Fasta To Genbank](https://www.biostars.org/p/2492/). As the title suggest, you will need your genome `gff3` and fasta reference as inputs.
Comments.UserDisplayName: Paul Endymion
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-01-10T14:26:51.220Z
Comments.Text: THanks for taking the time to consider my question Paul.  My gff3 files have the sequence in FASTA at the end of the file (following a ##FASTA indicator), but i take your point - will need some further leg work on this one!  Thanks for the link also.
Comments.UserDisplayName: Mark
Tags: <format-conversion><gff3><genbank>
Title: Existing tool for converting gff3 to genbank (gbk)
ThreadText: # Existing tool for converting gff3 to genbank (gbk)
  
  (Asked by: username_0 on 2020-01-09)
  
  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?
  
  **Tags:** format-conversion, gff3, genbank
  
  > **Comments:**
  > **username_1**: Hi there. I don't know any simple method for what you ask, mainly because `gff3` format does not contain sequences (only annotations) while `fasta` & `genbank` do. This thread on biostars might help tho :  [Gff3 + Fasta To Genbank](https://www.biostars.org/p/2492/). As the title suggest, you will need your genome `gff3` and fasta reference as inputs.  
  > **username_0**: THanks for taking the time to consider my question username_1.  My gff3 files have the sequence in FASTA at the end of the file (following a ##FASTA indicator), but i take your point - will need some further leg work on this one!  Thanks for the link also.  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2020-01-14. Score: 3
  
  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
  
  
  ---
  
  ### Answer by username_3 on 2020-01-13. Score: 1
  
  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.
  
  
  ---
  
  ### Answer by username_4 on 2022-07-16. Score: 1
  
  Here's a python script based on the [bcbio-gff](https://github.com/chapmanb/bcbb/tree/master/gff) (reading gff3) and [biopython](https://biopython.org/) (writing genbank): <https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py>
  
  > **Comments:**
  > **username_5**: just random ref, can `pip install bcbio-gff` and `pip install BioPython` to get these dependencies for this  
  
  ---
  
  