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beliveau-lab / OligoMiner

Genome-scale design tool for oligo hybridization probes
MIT License
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structureCheck.py cannot create multi-level temp dir #8

Closed ArielPaulson closed 4 years ago

ArielPaulson commented 4 years ago

Hi,

Temp dir creation needs to be "os.makedirs" not "os.mkdir", since input file may be have a path, which will cause the temp dir to be multi-level. Currently the script cannot create multi-level temp dirs.

Example, inside "OligoMiner/ExampleFiles:" location: Run: "python ../structureCheck.py -f 3_probes.bed -t 0.4"
Succeeds, because temp dir was only "/tmp/3_probes_432686".

Example, inside "OligoMiner" location: Run: "python structureCheck.py -f ExampleFiles/3_probes.bed -t 0.4", Dies, because cannot create temp dir "/tmp/ExampleFiles/3_probes_839260".

However if I first run "mkdir /tmp/ExampleFiles" and then run the above command, it succeeds.

Thanks, Ariel

brianbeliveau commented 4 years ago

Logic updated to support multi-level temp dirs.