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Hi, I am new using funannotate and I was trying to compare two annotated genomes with funannotate compare but I got this error.
[May 14 06:28 PM]: OS: Ubuntu 20.04, 256 cores, ~ 1057 GB RAM. Python…
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python Pangloss.py -h
File "Pangloss.py", line 334
print "{0}, {1} has unusual frameshift mutation and can't be run through yn00.".format(e, cluster)
^
SyntaxError: invalid syntax
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Does not seem to occur using Python 3.6.
Test failure as follows:
======================================================================
ERROR: test_correct_retrieval_1 (test_MafIO_index.TestSp…
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```R
> t1 is.rooted(t1)
[1] TRUE
```
but BioPython disagrees:
```python
>>> from Bio import Phylo
>>> t = Phylo.read('RAxML_bestTree.fastTrans_9.raxml', 'newick')
>>> t.rooted
False
```
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The instance was open and no installation (conda, python or anything) was taken. I proceeded straight to cloning BioCompass and installing it.
While running setup.py, the script presented the followi…
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While trying to run a full annotate + dn/ds:
python3 /home/pseudofinder/pseudofinder.py annotate --genome X.gbk --reference Y.gbk --database /home/plasmidfinder_db/DB.fasta --outprefix X
Im get…
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I've written a couple of fuzz tests and found a few (non-critical) bugs in some of the parsers. Before continuing any further is there any interest in accepting a PR with fuzz tests?
If you aren't …
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Could you please explain how the scripts in pyVCF/scripts work? (How to filter with those filters, how to make a new filter, anything really).
Documentation and Docs@http://pyvcf.readthedocs.io/en/la…
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Current dependence on python 3.7 is not maintainable as support for it is end of life as of end of 2023.
It also means that luna installation fails on Apple Silicon as python 3.7 is not available o…
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Hi Marco,
Thanks so much for making a really great package. I am going though the specified commands using the example Acinetobacter data provided in the supplemental data 3 from https://doi.org/10…