Answers.Body: <p>You're supplying a GTF feature file, but telling it that the features are in GFF3 format. I think you need <code>-fformat gff2</code>. See <a href="https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/" rel="nofollow noreferrer">https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/</a></p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-20T17:26:52.243Z
Answers.Text: I tried with gff2 but I get the same problem: Warning: bad /protein_id value 'CCQ26880'
  Warning: bad /protein_id value 'CCQ26881'
  Warning: bad /protein_id value 'CCQ26882'
  Warning: bad /protein_id value 'CCQ26883'
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-20T17:35:18.380Z
Answers.Text: If your copying the output directly, that's a different problem ('CCQ26880' vs. '''CCQ26880"'). It looks like it's parsing the GTF correctly but choking on the values for some reason. I'm not very familiar with this tool so I can't  advise further.
Answers.UserDisplayName: heathobrien
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-20T19:57:43.927Z
Answers.Text: Do you use another tool to get EMBL files from GTF and FASTA?
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-21T14:46:00.903Z
Answers.Text: @charlesdarwin have you tried this to convert FASTA -> EMBL? http://sequenceconversion.bugaco.com/converter/biology/sequences/embl_to_fasta.php (no idea of how it works, but you can try)
Answers.UserDisplayName: aechchiki
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-02-20T16:52:38.300Z
Answers.LastActivityDate: 2018-02-20T16:52:38.300Z
Answers.UserDisplayName: heathobrien
Body: <p>I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence:</p>
  
  <pre><code>seqret -sequence ecoli.fa -feature -fformat gff -fopenfile ecoli.gtf -osformat embl -auto -outseq ecoli.embl
  </code></pre>
  
  <p>It produces my desired EMBL file but it warns against a 'bad protein_id':</p>
  
  <pre><code>...
  Warning: bad /protein_id value '"CCE57732"'
  Warning: bad /protein_id value '"CCE57733"'
  Warning: bad /protein_id value '"CCE57734"'
  Warning: bad /protein_id value '"CCE57735"'
  Warning: bad /protein_id value '"CCE57754"'
  </code></pre>
  
  <p>What's wrong with these protein IDs? The organism I am working with is <em>Escherichia coli</em>.</p>
  
  <p>Here are a few lines from my GTF file. The first line has a protein_id.</p>
  
  <pre><code>Chromosome      ena     CDS     349     2808    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding"; protein_id "CCQ26880";
  Chromosome      ena     start_codon     349     351     .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  Chromosome      ena     stop_codon      2809    2811    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-19T14:06:56.143Z
Comments.Text: To me it looks like a bug, where the encoding or the quotes are not properly handled. (ie, CCE57754 would be a valid protien_id(?) but "CCE57754" it isn't)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-20T14:59:30.410Z
Comments.Text: Can you show (a small part of) your GTF file? I tend to agree with Llopis, but not all fields in the GTF files can be quoted.
Comments.UserDisplayName: Konrad Rudolph
Tags: <file-formats><format-conversion><gtf><emboss><seqret>
Title: seqret: Warning: bad /protein_id value
ThreadText: # seqret: Warning: bad /protein_id value
  
  (Asked by: username_0 on 2018-02-19)
  
  I am using the seqret tool from the Emboss suite to transform produce an EMBL annotation file from a GTF annotation file and the corresponding FASTA sequence:
  
  ```
  seqret -sequence ecoli.fa -feature -fformat gff -fopenfile ecoli.gtf -osformat embl -auto -outseq ecoli.embl
  
  ```
  
  It produces my desired EMBL file but it warns against a 'bad protein\_id':
  
  ```
  ...
  Warning: bad /protein_id value '"CCE57732"'
  Warning: bad /protein_id value '"CCE57733"'
  Warning: bad /protein_id value '"CCE57734"'
  Warning: bad /protein_id value '"CCE57735"'
  Warning: bad /protein_id value '"CCE57754"'
  
  ```
  
  What's wrong with these protein IDs? The organism I am working with is *Escherichia coli*.
  
  Here are a few lines from my GTF file. The first line has a protein\_id.
  
  ```
  Chromosome      ena     CDS     349     2808    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding"; protein_id "CCQ26880";
  Chromosome      ena     start_codon     349     351     .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  Chromosome      ena     stop_codon      2809    2811    .       +       0       gene_id "HUS2011_0001"; transcript_id "CCQ26880"; exon_number "1"; gene_name "thrA"; gene_source "ena"; gene_biotype "protein_coding"; transcript_name "thrA-1"; transcript_source "ena"; transcript_biotype "protein_coding";
  
  ```
  
  **Tags:** file-formats, format-conversion, gtf, emboss, seqret
  
  > **Comments:**
  > **username_1**: To me it looks like a bug, where the encoding or the quotes are not properly handled. (ie, CCE57754 would be a valid protien_id(?) but "CCE57754" it isn't)  
  > **username_2**: Can you show (a small part of) your GTF file? I tend to agree with Llopis, but not all fields in the GTF files can be quoted.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-02-20. Score: 1
  
  You're supplying a GTF feature file, but telling it that the features are in GFF3 format. I think you need `-fformat gff2`. See <https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/help/>
  
  > **Comments:**
  > **username_0**: I tried with gff2 but I get the same problem: Warning: bad /protein_id value 'CCQ26880' Warning: bad /protein_id value 'CCQ26881' Warning: bad /protein_id value 'CCQ26882' Warning: bad /protein_id value 'CCQ26883'  
  > **username_3**: If your copying the output directly, that's a different problem ('CCQ26880' vs. '''CCQ26880"'). It looks like it's parsing the GTF correctly but choking on the values for some reason. I'm not very familiar with this tool so I can't  advise further.  
  > **username_0**: Do you use another tool to get EMBL files from GTF and FASTA?  
  > **username_4**: @charlesdarwin have you tried this to convert FASTA -> EMBL? http://sequenceconversion.bugaco.com/converter/biology/sequences/embl_to_fasta.php (no idea of how it works, but you can try)  
  
  ---
  
  