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Bioinformatics

Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.

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peterjc
peterjc commented Dec 18, 2018

Setup

Seen with latest code from git while preparing the 1.73 release on Linux, but applies to all platforms.

Expected behaviour

$ python run_tests.py test_PDB_StructureAlignment.py
Python version: 2.7.15 | packaged by conda-forge | (default, Jul 27 2018, 10:26:36) 
[GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
Operating system: posix linux2
test_PDB_StructureAlignment ... ok
samuell
samuell commented Aug 27, 2020

Analogous to how you can use basename to get only the filename of a path, like in:

p.SetOut("out1", "{i:in1|basename}.out.txt")

... it would be useful to also be able to extract only the directory, using dirname as a modifiers, so:

p.SetOut("out1", "{i:in1|dirname}/newfilename.txt")

This will also allow introducing another level of folders based on a previous

scanpy
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