Converts to embl but with interrogation marks in SQ

[nbisweden]

Converts to embl but with interrogation marks in SQ

[Juke34]

Your gff annotation contains annotations attached to a sequence that is absent from the fasta file provided. So it creates a unknown sequence (with ??? because it cannot guess the DNA sequence) with the lenght corresponding to the position of the last feature found on it. Check your fasta file, it shoiuld be the same as used for the annotation.

Otherwise you can filter the annotations not attached to sequences present in the fasta file using the script gff3_sq_keep_annotation_from_fastaSeq.pl from the GAAS toolkit

[Iseez]

Thanks, that worked.

Just one question more, when i was tryng to obtain the embl for a different species i encountered the following error:

Traceback (most recent call last):                                             ]
  File "/cm/shared/apps/emblmygff3/1.2.6/bin/EMBLmyGFF3", line 11, in <module>
    load_entry_point('EMBLmyGFF3==1.2.6', 'console_scripts', 'EMBLmyGFF3')()
  File "/cm/shared/apps/emblmygff3/1.2.6/lib/python2.7/site-packages/EMBLmyGFF3-1.2.6-py2.7.egg/EMBLmyGFF3/EMBLmyGFF3.py", line 1383, in main
    writer.write_all( outfile )
  File "/cm/shared/apps/emblmygff3/1.2.6/lib/python2.7/site-packages/EMBLmyGFF3-1.2.6-py2.7.egg/EMBLmyGFF3/EMBLmyGFF3.py", line 1179, in write_all
    self._add_mandatory()
  File "/cm/shared/apps/emblmygff3/1.2.6/lib/python2.7/site-packages/EMBLmyGFF3-1.2.6-py2.7.egg/EMBLmyGFF3/EMBLmyGFF3.py", line 195, in _add_mandatory
    if seq[end] == 'n' :
IndexError: string index out of range

Is the problem due to the files I'm using as input?

[Juke34]

The original question is resolved. I close this issue. I created a new issue reporting the other problem you are encountered => see #38