apologies if this is a basic question, but I couldn't seem to find a clear cut solution. I'm using a global recursive search to find a file with a specific extension in a directory and it's subdirectories, like so:
my code
bam = list(Path('path/to/file').rglob("*.bam"))
This returns something like:
[PosixPath('path/to/file/file.bam')]
However, I want to extract just the filepath, so that bam variable is a string contains just the file path, i.e.
bam = 'path/to/file/file.bam'.
I realize I could probably convert the current output to a string, and then use regex to extract everything between the ' ' but I'm hoping there's a more elegant way, or even a simpler solution to recursively search files for different extensions and outputting a filepath as a string!
As always, any help is appreciated!
rglob return a generator which yields references to objects that are subclasses of PurePath. Those objects will reveal the actual pathname via their implementation of __str__(). Therefore:
from pathlib import Path
for p in Path('path/to/file').rglob('*.bam'):
print(p)
...will almost certainly give what you're looking for.
Bear in mind that print() will implicitly invoke an object's str() function (if available). If you need to get the filenames into a list then you would need to explicitly call str(). For example:
lop = [str(p) for p in Path('path/to/file').rglob('*.bam')]