PyNucamino
Python bindings for nucamino
Installation
pip install pynucamino should work on MacOS, Windows, and Linux
systems. The package includes the nucamino binaries, so you don't
need to install anything else.
Usage
>>> import pynucamino
>>> pynucamino.Nucamino.profiles()
["hcv1a", "hcv1b", "hcv2", "hcv3", "hcv4", "hcv5", "hcv6", "hiv1b"]
>>> test_sequence = """> Test Sequence
... GATTACA"""
>>> pynucamino.align(test_sequence, "hcv1a", ["NS3"])
...
# Alignment Results
>>> pynucamino.align_file("input_filename.fasta", "hcv1a", ["NS5B"])
...
# Alignment Results
>>> alignment = pynucamino.Nucamino(test_seq, profile="hcv1a", genes=["NS3"])
>>> alignment.result
...
# Alignment Results
>>> alignment.proc
...
# subprocess.CompletedProcess Use pynucamino.align or pynucamino.align_file to align a FASTA
formatted collection of sequences in a string or a file, repsectively.
For more fine-grained control, the pynucamino.Nucamino class has
result property containing the alignment results and a proc
property that contains details on exactly how nucamino was called.
Use the built-in help function for more information on each class
and function.
Security Warning
This library is probably vulnerable to command injection when run with malicious inputs. If you care at all about the security of your system, you shouldn't use this library unless you trust whoever is setting the parameters.
In practice, this means that setting up a web-server that runs this library using input from anonymous users on the public internet might get your systme hacked. The intended use case is writing internal scripts that are run with pre-determined parameters; this case is perfectly safe.
