A small dirty script to get a mapping from Gold Stamp ID from JGI to an SR-ID easity downloadable by fastq-dump.
Really convinent if you want to use the metagenomic libraries used in Nayfach et al 2020's for further analysis, about half of the libraries can be obtained with this. Probably more could be obtained with more clever queries, but I am lazy, and it was good for my purposes.
Can easily be modified to obtain other samples.
Also, JGI provides similar files here https://gold.jgi.doe.gov/downloads
Needs biopython, easily installable with pip install biopython for example
python jgi2sra_mapper.py NCBI_USER GOLD_IDS OUTPUT_FILE
with NCBI_USER the email you use to log into NCBI, GOLD_IDS a text file with a 'Gold Stamp ID', typically an ID from IMG/JGI starting with Gp, the file provided with this archive (GEMs_metagenomes_ids.txt) is the third column of Supplemental Table 1 of Nayfach et al 2020 OUTPUT_FILE is the name of the file you want the output saved in (the output gold2sra.json is the one generated with GEMs_metagenomes_ids.txt).
Thanks Maliheh Mehrshad, Julia Nuy, Alejandro Rodriguez Gijón and Sarahi L. Garcia, as well as the whole team at IMG/JGI, and the authors of Nayfach et al 2020 for the 'inspiration' for this...
Nayfach, S., Roux, S., Seshadri, R. et al. A genomic catalog of Earth’s microbiomes. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0718-6 Also, JGI provides similar files here https://gold.jgi.doe.gov/downloads
You can cite this through the DOI : 10.17044/scilifelab.13246817