Web of Life project peptide sequence subsampling script

Objective

Obtain peptide sequences for a manageable sampling of prokaryotic genomes for small-scale comparative genomics and/or phylogenetics analyses.

Rationale

Inclusive databases such as the NCBI nr database contain data for so many prokaryotic genomes, that obtaining sequences from a representative sampling of bacteria or archaea via NCBI's Basic Local Alignment Search Tool (BLAST) or other means becomes difficult without restricting searches to a relatively small selection of genomes. However, selected genomes must be representative for the taxonomic scope of interest, being relatively complete and high quality, otherwise comparative genomics results will be compromised.

Zhu et al. describe a systematic selection of representative prokaryotic genomes in this article:

Zhu, Q., Mai, U., Pfeiffer, W., Janssen, S., Asnicar, F., Sanders, J.G.,
Belda-Ferre, P., Al-Ghalith, G.A., Kopylova, E., McDonald, D., Kosciolek,
T., Yin, J.B., Huang, S., Salam, N., Jiao, J.-Y., Wu, Z., Xu, Z.Z.,
Cantrell, K., Yang, Y., Sayyari, E., Rabiee, M., Morton, J.T., Podell, S.,
Knights, D., Li, W.-J., Huttenhower, C., Segata, N., Smarr, L., Mirarab,
S., Knight, R., 2019. Phylogenomics of 10,575 genomes reveals evolutionary
proximity between domains Bacteria and Archaea. Nat Commun 10, 5477.
https://doi.org/10.1038/s41467-019-13443-4

They provide a data sheet of information about each of the genomes they selected, including taxonomic information and information on assembly quality, etc. here:

https://biocore.github.io/wol/data/genomes/metadata.tsv.bz2

They describe how to retrieve their genome and protein data here (you have to use Globus):

https://biocore.github.io/wol/data/genomes/

For smaller-scale comparative genomics studies, it will be necessary to obtain a subsampling of these 10,575 representative genomes in a systematic manner according to measures of quality and taxonomic diversity. That is what this script does.

Software requirements

Linux or MacOS operating system
Python3
The pandas python library
Git
bzip2

Procedure

Obtain the per_genome.tar file containing peptide sequence FASTA files from here via Globus: https://app.globus.org/file-manager?origin_id=31acbeb8-c62f-11ea-bef9-0e716405a293&origin_path=%2Fproteins%2F
Decompress the tar file.

Clone this repository.

git clone https://github.com/laelbarlow/wol_peptide_subsampler.git

Change directories into the repository.
```
cd wol_peptide_subsampler
```
Subsample the protein sequence files according to measures of quality and taxonomic diversity (as detailed in the TSV file).
```
python3 subsample_wol_peptides.py <path to per_genome dir>
```
Examine the CSV file with information for only the subsampled genomes here:
```
results/metadata_subsample.csv
```
Proceed with downstream analysis of the selected peptide FASTA files here:
```
results/peptide_seqs_subsample/
```

License

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.