Comments (5)
Could you share your command line?
I will have a look when I will find time.
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I tested with the test coming with the tool (EMBLmyGFF3-augustus-example
). It shows the command. I added --locus_numbering_start 30
and it works for me, I get
gene 386..13142
FT /locus_tag="MYLOCUSTAG_LOCUS30"
for the first gene and
FT gene 16086..38972
FT /locus_tag="MYLOCUSTAG_LOCUS31"
for the second...
from emblmygff3.
Thanks for the speedy answer and this great tool.
Indeed, it works fine for me too after adapting the EMBLmyGFF3-augustus-example
but it still fails though with the EMBLmyGFF3-prokka-example
.
from emblmygff3.
Right, I guess it is because Prokka file already contains the locus_tag
attributes.
You can remove/rename them prior to run the conversion.
sed `s/locus_tag=/locus_tag_original=/g` yourfile.gff > yourfile_fixed.gff
from emblmygff3.
Thanks this solves indeed the problem.
It would be great though to have an option for being able to set a different incremental step than 1.
from emblmygff3.
Related Issues (20)
- How to add in comment or CC line HOT 1
- Webin-CLI validation failing due to duplicated feature locations in EMBLmyGFF3 flat file HOT 2
- thank you HOT 1
- ImportError Bio.Alphabet error HOT 1
- What the option "-a accesion" parameter should to be set(means:What type?) HOT 3
- TypeError: read() takes 1 positional argument but 2 were given? HOT 3
- attribute formats broken across several lines HOT 2
- Use of example data HOT 2
- Contigs are disorganised in the EMBL file HOT 10
- Warning qualifier unknown db_xref HOT 1
- Translation problem HOT 2
- Reporting the line number of the problematic input GFF3 files when parsing error is triggered HOT 2
- BioPython 1.81 installs via conda, but needs an older version HOT 2
- if I can specify certain python source during python setup.py install HOT 2
- Not for ENA submission: Sequence too short
- Installation issue EMBLmyGFF3 & python version requirements
- Translation when circular genome and ORF in the cut of the assembly HOT 1
- unexpected keyword argument 'strand' HOT 3
- Gene sorting compared to fasta HOT 4
- Bug when specifying -g mitochrondrion (or plastid)
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