updating runinfo CSV -

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search at https://www.ncbi.nlm.nih.gov/sra/ for "METAGENOMIC"[Source] NOT amplicon[All Fields]

direct link courtesy of luiz:

https://www.ncbi.nlm.nih.gov/sra/?term=%22METAGENOMIC%22%5BSource%5D%20NOT%20amplicon%5BAll%20Fields%5D

to download file:

send to... summary.

consider updating file https://osf.io/download/762mk/ referenced over at https://github.com/sourmash-bio/2022-search-sra-with-mastiff/blob/main/interpret-sra-live.ipynb

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planning to keep latest runinfo here on farm:

~ctbrown/transfer/sra-runinfo-latest.tar.gz

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so I am very confused about all of this 😆 - the runinfo file produced by the above contains the following headers:

"Experiment Accession","Experiment Title","Organism Name","Instrument","Submitter","Study Accession","Study Title","Sample Accession","Sample Title","Total Size, Mb","Total RUNs","Total Spots","Total Bases","Library Name","Library Strategy","Library Source","Library Selection"

but I also want these headers which come from ...somewhere else and are per-run. Working on it.

Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,LibrarySource,LibraryLayout,InsertSize,InsertDev,Platform,Model,SRAStudy,BioProject,Study_Pubmed_id,ProjectID,Sample,BioSample,SampleType,TaxID,ScientificName,SampleName,g1k_pop_code,source,g1k_analysis_group,Subject_ID,Sex,Disease,Tumor,Affection_Status,Analyte_Type,Histological_Type,Body_Site,CenterName,Submission,dbgap_study_accession,Consent,RunHash,ReadHash

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ok, when sending to file select 'Run Info'. Doesn't work for whole thing but.

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this is useful: https://eaton-lab.org/articles/sra-downloads/

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also via taylor: https://github.com/nf-core/fetchngs/blob/c318ae12fcb972ff28f6d38edd3165c88b6d0b3f/bin/sra_ids_to_runinfo.py

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aaaaand maybe we should be using bigquery (or NCBI wants us to use it, whichever) - https://www.ncbi.nlm.nih.gov/sra/docs/sra-bigquery/

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ok finally found my code for doing this on a sample by sample basis -

https://github.com/dib-lab/2022-sra-gather/blob/main/summarize-sample.py

run here:

https://github.com/dib-lab/2022-sra-gather/blob/main/Snakefile

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the shell script at the bottom here: https://www.seqanswers.com/forum/bioinformatics/bioinformatics-aa/74666-downloading-runinfo-table-from-sra-run-selector is useful