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CCB-SB / plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI
https://ccb-microbe.cs.uni-saarland.de/plsdb/
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README.md for PLSDB v. 2021_06_23 #15

Closed haruosuz closed 1 year ago

haruosuz commented 2 years ago

https://ccb-microbe.cs.uni-saarland.de/plsdb/plasmids/download/

A README file is also provided explaining the content and formatting of all included files.

Where can I download the README file?

The META archive and FASTA archive were downloaded on 2022-02-02 using:

wget https://ccb-microbe.cs.uni-saarland.de/plsdb/plasmids/download/plasmids_meta.tar.bz2
tar -jxvf plasmids_meta.tar.bz2
wget https://ccb-microbe.cs.uni-saarland.de/plsdb/plasmids/download/plsdb.fna.bz2
bunzip2 -c plsdb.fna.bz2 > plsdb.fna
VGalata commented 2 years ago

I can confirm that the README file is missing in the "meta" archive.

@SmalJonni It seems that this files was forgotten. Maybe in the future the README could be also included in this repository to track changes and to provide a copy of the description of the data?

SmalJonni commented 2 years ago

Thank you for reporting the issue.

I will think about a solution that automatically includes the README.md of the meta archive in the README.md of this repository, so the file only has to be updated once. Accordingly, I will leave the issue open for now.

haruosuz commented 2 years ago

pMCBF1 (AY950444) is not included in PLSDB v. 2021_06_23_v2.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104523/ pMCBF1 formed a novel clade, hereafter called ζ. Sequences of pMCBF1 and pMCBF6 were deposited in GenBank; Nucleotide Core #(accession AY950444 and EF107516).

SmalJonni commented 2 years ago

Thank you for reporting the issue. We can confirm that the plasmid is not included. The plasmid is not picked up during data collection due to an incorrect organism specification. We are currently looking into possible solutions.