KeyError: 'animal_mt' about getorganelle HOT 5 CLOSED

Thanks for pointing out this bug. I will fix this very soon.
Currently, you could rename Astalotermes_gene_features_sequence.txt to animal_mt.fasta and make it work (if you use --continue option to resume, you should firstly remove *csv files previously produced). I would let you know once I fixed this, after which there is no need to do this pre-renaming.
Sorry for the inconvenience and thanks again for letting me know!

Best,
Jianjun

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Hello Jianjun,

Thanks, it did work indeed!

Cheers,
Simon

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Fix it in 1.6.2a. No need to rename anymore.
But I am in the field these days and only get a small dataset to test. Let me know if it doesn't work for you.

Cheers,
Jianjun

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Dear Jianjun,

I have a little question, what exactly does -- genes mean, while you enter a command.

I can't find an explanation in the help.

Looking forward to your help.

Thanks.

from getorganelle.

Dear Jianjun,

I have a little question, what exactly does -- genes mean, while you enter a command.

I can't find an explanation in the help.

Looking forward to your help.

Thanks.

You can type get_organelle_from_reads.py --help rather than get_organelle_from_reads.py -h to get a verbose version of all options, where you can find illustration of --genes as follows:

--genes=GENES_FASTA
                   Followed with a customized database (a fasta file or
                   the base name of a blast database) containing or made
                   of ONE set of protein coding genes and ribosomal RNAs
                   extracted from ONE reference genome that you want to
                   assemble. Should be a list of databases split by
                   comma(s) on a multi-organelle mode, with the same list
                   length to organelle_type (followed by '-F'). This is
                   optional for any organelle mentioned in '-F' but
                   required for 'anonym'. By default, certain database(s)
                   in /Users/Kinggerm/.pyenv/versions/anaconda3-5.3.1/lib
                   /python3.7/site-packages/GetOrganelleLib/LabelDatabase
                   would be used contingent on the organelle types chosen
                   (-F). The default value no longer holds when '--genes'
                   or '--ex-genes' is used.

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