Comments (3)
It was working with biopython 1.76. Could you try to downgrade biopython to 1.77.
Let me know if it works. If yes I will update the conda recipe accordingly.
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I ended up installing with a local environment file via conda env create -f myEMBLmyGFF3.yml
. This seems to have solved the issue, at least I was able to run the maker example files.
The yml file:
name: EMBLmyGFF3
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- python >=3
- biopython =1.67
- bcbio-gff =0.6.4
- numpy <1.16.5
- emblmygff3
Thanks!
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And checked and yes Bio.Alphabet has been removed from Biopython 1.78 (September 2020).
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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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