MSA application default options

[EiriniKot]

Do you know which are the default options for biotite - mafft, clustal-omega and muscle? ( Or where can I find them)

[padix-key]

Hi. Like all LocalApp subclasses, The MSA software interfaces have the get_command() method, that returns the executed command, including all used options.

[EiriniKot]

I am using this object :biotite.application.mafft.MafftApp (https://www.biotite-python.org/apidoc/biotite.application.mafft.MafftApp.html)

aligner_app
PyDev console: starting.
<class 'biotite.application.mafft.MafftApp'>


aligner_app.get_command()
Traceback (most recent call last):
  File "/snap/pycharm-professional/359/plugins/python/helpers/pydev/_pydevd_bundle/pydevd_exec2.py", line 3, in Exec
    exec(exp, global_vars, local_vars)
  File "<input>", line 1, in <module>
  File "/home/eirini/anaconda3/envs/gaz-torch-cuda/lib/python3.8/site-packages/biotite/application/application.py", line 52, in wrapper
    instance = args[0]
IndexError: tuple index out of range

[padix-key]

From your output it seems you called get_command() on the MafftApp class instead of an MafftApp object. However, get_method() is an instance method, and it must be, since the command depends on how the created MafftApp object is configured. So this should work:

seq1 = ProteinSequence("BIQTITE")
seq2 = ProteinSequence("TITANITE")
seq3 = ProteinSequence("BISMITE")
seq4 = ProteinSequence("IQLITE")
app = MafftApp([seq1, seq2, seq3, seq4])
app.start()
app.join()
print(app.get_command())

Nonetheless, I admit a clearer error message would be helpful here.

[EiriniKot]

I am using align function to do the alignment instead of app = MafftApp([seq1, seq2, seq3, seq4]) so basically I am creating the app instance from MafftApp and then I do app.align([seq1, seq2, seq3, seq4])

[padix-key]

Could you paste your code? The output shown above indicates that aligner_app is the class MafftApp and not an object:

<class 'biotite.application.mafft.MafftApp'>

Hence, calling aligner_app.get_command() fails.

[EiriniKot]

aligner_app = mafft.MafftApp
aligner_app.align([seq1,seq2,seq3,seq4])
Alignment([ProteinSequence("BIQTITE"), ProteinSequence("TITANITE"), ProteinSequence("BISMITE"), ProteinSequence("IQLITE")], np.array([[-1,  0, -1, -1],
       [ 0,  1,  0, -1],
       [ 1,  2,  1,  0],
       [ 2,  3,  2,  1],
       [ 3,  4,  3,  2],
       [ 4,  5,  4,  3],
       [ 5,  6,  5,  4],
       [ 6,  7,  6,  5]]), score=None)
aligner_app.get_command()
Traceback (most recent call last):
  File "/snap/pycharm-professional/359/plugins/python/helpers/pydev/pydevconsole.py", line 364, in runcode
    coro = func()
  File "<input>", line 1, in <module>
  File "/home/eirini/anaconda3/envs/gaz-torch-cuda/lib/python3.8/site-packages/biotite/application/application.py", line 52, in wrapper
    instance = args[0]
IndexError: tuple index out of range

[padix-key]

The problem is the first line:

aligner_app = mafft.MafftApp

aligner_app is assigned to the class, not to an object of it. This is OK for simply aligning, since you use the shortcut static method align() that is called on the class itself. However, to be able to get the command you need to run it based on a created object. So this would be the modification:

aligner_app = mafft.MafftApp([seq1,seq2,seq3,seq4])
aligner_app.start()
aligner_app.join()
print(aligner_app.get_command())
print(aligner_app.get_alignment())

I would recommend the object-based API, if specific parameters should be given to an Application or side results (such as the command) should be obtained from the application run.

[EiriniKot]

thank you