sra_metadata as standalone function that creates `metadata.yaml` sheet
Closed this issue · 2 comments
aguang commented
See #41 for some context.
We want to split out sra_metadata.py
so that it actually is a standalone python script that will create a metadata.yaml
sheet from querying SRA, for qcdb.db_load
to parse and load. It will take as input a path to a data folder, and an output path where metadata.yaml
will go. The data folder should have either SRR
ids as generated from sra-tools
/fasts-dump
, or SRX_SRS
ids as generated from bioflows
.
aguang commented
For a sheet that's based on data from SRA, db_id
should be filled out as an SRS_SRX
id, and it should also have fields sample_id
: SRS
and experiment_id
: SRX
.
j-stat commented
All set and pushed to GitHub