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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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Add support for downloading GEO files #129

Closed DevangThakkar closed 3 years ago

DevangThakkar commented 3 years ago

Fixes Issue #120.

The -g argument allows downloads of GEO files. This argument can also be used concurrently with -p. The commands shown below are some valid uses of the argument:

# download GEO files for GEO ID GSE161707
pysradb -g GSE161707

# download GEO files for GEO IDs GSE161707 and GSE161708
pysradb -g GSE161707 GSE161708

# download GEO files for GEO ID GSE161707 and SRA files for SRP ID SRP016501
pysradb -g GSE161707 -p SRP016501
DevangThakkar commented 3 years ago

Hi Saket, running flake8 locally gives a lot of warnings/errors for the existing codebase so it would be useful if you could recap the style conventions that you use/recommend in this project, thanks!

saketkc commented 3 years ago

Many thanks for the PR @DevangThakkar! I will take a deeper look soon, but we use black, so you would have to do black . in the pysradb directory.

codecov[bot] commented 3 years ago

Codecov Report

Merging #129 (8d68e97) into master (14ddbfb) will increase coverage by 1.85%. The diff coverage is 78.18%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #129      +/-   ##
==========================================
+ Coverage   56.51%   58.37%   +1.85%     
==========================================
  Files           7        8       +1     
  Lines        1718     1773      +55     
==========================================
+ Hits          971     1035      +64     
+ Misses        747      738       -9
Impacted Files Coverage Δ
pysradb/cli.py 0.00% <0.00%> (ø)
pysradb/geoweb.py 93.47% <93.47%> (ø)
pysradb/sraweb.py 83.13% <0.00%> (+3.17%) :arrow_up:
pysradb/download.py 28.39% <0.00%> (+5.89%) :arrow_up:

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saketkc commented 3 years ago

Thanks once again @DevangThakkar! I was unaware of files.txt existence, pretty nice!

DevangThakkar commented 3 years ago

You're welcome @saketkc! Feel free to assign me to future issues. (: