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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
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Cache directories created for all releases, not just requested release #241

Closed dhimmel closed 3 years ago

dhimmel commented 3 years ago

When I run the following:

pyensembl install --release=100 --species=human

I get a cache directory for every ensembl release:

/home/jovyan/work/data/.data_source_cache/pyensembl/GRCh37:
total 92K
drwxr-sr-x 23 jovyan users 4.0K Aug 21 19:35 ./
drwxr-sr-x  5 jovyan users 4.0K Aug 21 19:35 ../
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl55/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl56/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl57/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl58/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl59/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl60/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl61/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl62/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl63/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl64/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl65/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl66/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl67/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl68/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl69/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl70/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl71/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl72/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl73/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl74/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl75/

/home/jovyan/work/data/.data_source_cache/pyensembl/GRCh38:
total 108K
drwxr-sr-x 27 jovyan users 4.0K Aug 21 19:35 ./
drwxr-sr-x  5 jovyan users 4.0K Aug 21 19:35 ../
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:40 ensembl100/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl76/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl77/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl78/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl79/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl80/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl81/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl82/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl83/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl84/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl85/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl86/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl87/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl88/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl89/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl90/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl91/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl92/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl93/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl94/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl95/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl96/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl97/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl98/
drwxr-sr-x  2 jovyan users 4.0K Aug 21 19:35 ensembl99/

All of these directories are empty besides pyensembl/GRCh38/ensembl100. I think it's ideal to avoid cluttering the file system and only creating these directories when they are first needed.

iskandr commented 3 years ago

Yikes: 

ensembl100/  ensembl77/  ensembl79/  ensembl81/  ensembl83/  ensembl85/  ensembl87/  ensembl89/  ensembl91/  ensembl93/  ensembl95/  ensembl97/  ensembl99/
ensembl76/   ensembl78/  ensembl80/  ensembl82/  ensembl84/  ensembl86/  ensembl88/  ensembl90/  ensembl92/  ensembl94/  ensembl96/  ensembl98/

I'll look into this.

iskandr commented 3 years ago

OK, should be fixed :

ensembl100  ensembl77  ensembl93