Converting gff3 to embl

Converting gff3 to embl

It was alway a pain for me to work with the embl format. Unfortunately for using Artemis and ACT I need embl files again. Tried to install EMBLmyGFF3 with biopython > 1.67 on my laptop.

EMBLmyGFF3 requires Python 2.7 and biopython 1.67

Python setup virtual environment

Using Python 2.7

mkdir ~/pyvenv
virtualenv ~/pyvenv/emblmygff

source ~/pyvenv/emblmygff/bin/activate

Download biopython 1.67 source file (https://biopython.org/wiki/Download)

To install from source (on Mac):

xcode-select --install

enter the source directory and try

python setup.py build
python setup.py test
python setup.py install

install EMBLmyGFF3

pip install git+https://github.com/NBISweden/EMBLmyGFF3.git

Finally it indicated that the tools was install successfully

Successfully installed EMBLmyGFF3-1.2.4 bcbio-gff-0.6.4 biopython-1.67 six-1.12.0

(emblmygff) mib110701i:biopython-1.67 zl3$ EMBLmyGFF3 -h

Works!!

To check installed packages: use

pip freeze

which shows:

bcbio-gff==0.6.4
biopython==1.67
EMBLmyGFF3==1.2.4
six==1.12.0

Commands of EMBLmyGFF3 with essential options:

EMBLmyGFF3 chr7.gff Smansoni.fa -s 'Schistosoma mansoni' -i Smp -m 'genomic DNA' -p PROJ000 -t linear -r 1 -o chr7.embl

Where

-s species

-i locus_tag

-m molecule_type

-p project_id

-t topology (linear/circular)

-r transl_table

Finally to leave the vitural environment type: deactivate

Z. Lu avatar
Z. Lu
Computer biologist, amature photographer, vintage fan and web lover.
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