PHANOTATE
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deprekate
PHANOTATE: a tool to annotate phage genomes.
Running phanotate on some phage gives me this error. The below is from [Hubei odonate virus 11](https://www.ncbi.nlm.nih.gov/nuccore/NC_032956): ```bash (phan.env) [jmeppley@tyrosine phanotate]$ phanotate.py -o test/NC_032956.ncbi.faa -f fasta test/NC_032956.ncbi.fasta /mnt/data0/jmeppley/projects/nanopore_biller/viemes_by_depth/phage_clusters/phanotate/phan.env/bin/phanotate.py:4: DeprecationWarning: pkg_resources...
Hi Do you have any plan to upload the newest version on bioconda repository ? Thanks
How do you output a protein fasta (.faa)? Also, I keep getting an error for start/stop options? Do I use prodigal on the orfs this calls?
Hello, We are noticing that the ORFs called in 1.5.1 are different than 1.6.1. Also, we are seeing +, *, and # randomly being put in sequences in 1.6.1. I...
Hi Katelyn, thanks for PHANOTATE, great tool! I'm using it for larger sets of viral contigs, and noticed that it seems to not free up RAM between contigs. On my...
Hi, I recently annotated phages with phanotate in an environment where tRNAscan-SE was installed. Therefore, tRNA masking did use tRNAscan-SE. However, in my final NCBI submission I also added tRNA...
Hi, I am encountering cases where there are truncated proteins (missing stop codon) called by phanotate at the genome end. The common case was when there was another protein on...
The `develop` branch has two output errors: 1. Genbank files (printed to STDOUT) occasionally contain an additional line of the format: ``` 92033_gap 92355_gap ``` 2. fasta files (whether to...
Can you please link to [zenodo](https://www.zenodo.org/) and then make a new release and you will get a DOI. Then you can add the badge, too
Dear deprekate Thank you so much for developing this, I'm sure it'll come extremely useful for anyone interested in phages :) Just wanted to ask you if PHANOTATE is suitable...
