Jacques Dainat
We didn’t implement a way to do so by the command line interface. You will have to add this information after the conversion within the embl file using a bash...
This is not on our todo list currently. Independent approaches can be used to perform this task (e.g. using bioperl, biopython) but it's something that could be implemented in a...
Bio.Alphabet has been removed from Biopython 1.78 (September 2020). You should downgrad biopython to a previous version.
I will investigate that once I will be back from vacation.
^^ Thank you for your feedback Glad to hear you enjoy the tool.
As long as it is not implemented within EMBLmyGFF3, using the perl script `agat_sp_flag_short_introns.pl` from the [AGAT](https://github.com/NBISweden/AGAT) repo does the job.
maybe avoiding in the FEATURE object self._load_qualifier_translations(Feature.DEFAULT_QUALIFIER_TRANSLATION_FILE + translation_files) self._load_feature_translations(Feature.DEFAULT_FEATURE_TRANSLATION_FILE) for every feature but only once at the beginning will save lot of time.
Are you using version2? You can try version3 which is in the branch feature/speedup but not all features are implemented. This version is multithreaded. Otherwise you can split you files...
Hi @AdamStuckert, I have made an update of the version 2 to make it faster (it is on branch "speed"). It is not multi threaded but might be 10X faster....
Hi @AdamStuckert, did you succeed to run the tool from the speed branch? Did you see any improvement in term of time?