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
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piping support #8

Closed saketkc closed 4 years ago

saketkc commented 5 years ago

From: https://doi.org/10.5256/f1000research.20450.r47560

One frustrating limitation is that the piping support is not univeral throughout the tool. You can pipe into the download command, but not, for example, into the metadata command. Being able to chain operations such as:

pysradb gse-to-srp GSE24355 | pysradb metadata | pysra download

..or

pysradb search '"oocyte development"' | head | pysradb metadata

..would be really nice and presumably not too hard to support?