search

saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
307 stars 50 forks source link

KeyError: 'run_accession' #167

Closed ChongLC closed 1 year ago

ChongLC commented 1 year ago

I tried testing running SRAweb using Colab for SRR11378996. It popped out an error (as shown below). image

While checking the ncbi SRA, it provides the information as shown here: https://www.ncbi.nlm.nih.gov/sra/?term=SRR11378996.

May I know how should I solve this?

Looking forward to hearing from you. Thank you.

Regards, Chong

saketkc commented 1 year ago

Thank you for the bug report. I have pushed a fix in https://github.com/saketkc/pysradb/commit/bb6d46226c04234b30eaa935cd6644c8f9cbce3f

Unfortunately for this project NCBI does not return all the run ids (possibly because there are 700+), so only experiment accession and related metadata is reported. See notebook here: https://colab.research.google.com/drive/1Z_lrhf3hUru1nBbLKoPeHM6RLxidiyni?usp=sharing

ChongLC commented 1 year ago

Thank you for the explanation @saketkc!