where it says that the sample is from pathogenic bacteria in the SRA database? for example, I want to download only SRA samples of a pathogenic Acinetobacter baumannii. is there some filter for that?
I am assuming that by pathogenic you mean that the host is listed as human in NCBI Taxonomy. In such a situation, you should start at NCBI Taxonomy with the following query: Acinetobacter baumannii[Name Tokens] AND "host human"[Properties]. You will see 312 results. Click on the drop-down list under "Find related data" and choose "SRA". This will return 208 SRA results.
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I think your best chance is to browse Pubmed for relevant publications and then search for the respective datasets. Relying on just an SRA entry that says "pathogenic" is quiet risky. Better go for the paper, read and check if he samples really are what you need and then proceed. Without a proper methods text, you barely have an idea of what data you are dealing with.
thank you for your answer, but I am looking for a way to do this thing automatically by writing a bash script that would download for me full bacterias genome using SRA entries, and the input is just a bacteria full name. I need also to find a way to separate the genomes to a pathogen and not pathogen bacteria. I don't see how I could use PubMed for that.
You can limit SRA search to organism or taxonomy ID of interest, for example, https://www.ncbi.nlm.nih.gov/sra?term=%22Acinetobacter%20baumannii%22%5BOrganism%5D%20&cmd=DetailsSearch