Flye assembler should support spaces in file paths.

mikolmogorov / Flye

De novo assembler for single molecule sequencing reads using repeat graphs

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Flye assembler should support spaces in file paths. #693

Closed sarahjeeeze closed 2 months ago

sarahjeeeze commented 2 months ago

Although users should not have spaces in file and directory names it is fairly common and other tools support it. It would be great if Flye could support such files.

Currently Flye will return eg [2024-04-08 09:25:14] ERROR: Path to reads contain spaces: https://github.com/fenderglass/Flye/blob/21a7191dc39796d83afd5b6d1b387800a9f64380/flye/main.py#L421

mikolmogorov commented 2 months ago

It is - in general - bad practice to have spaces in flie path at UNIX-lie systems. It is an easy change to make on the user side, so I am not currently planning to add support for that.