How to define MSA path?

[kerbychok]

Hi,
I am trying to do a sequence alignment using the application subpackage. I have 'installed' the necessary binaries, for example the MUSCLE and Clustal Omega binaries. I tried to define the path for muscle using the bin_path argument as shown below. I am using windows 10.

import biotite.application.muscle as muscle
import biotite.sequence as seq
seq1 = seq.ProteinSequence("BIQTITE")
seq2 = seq.ProteinSequence("TITANITE")
seq3 = seq.ProteinSequence("BISMITE")
seq4 = seq.ProteinSequence("IQLITE")
app = muscle.MuscleApp(sequences = [seq1, seq2, seq3, seq4], bin_path = "C:\\Users\\Work\\anaconda3\\Lib\\site-packages\\biotite\\application\\muscle\\muscle-5.0.1428\\binaries\\muscle." )
app.start()
app.join()
alignment = app.get_alignment()
print(alignment)

This is the error i receive.

SubprocessError                           Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_8208/2709834208.py in <module>
      8 app = muscle.MuscleApp(sequences = [seq1, seq2, seq3, seq4], bin_path = "C:\\Users\\Work\\anaconda3\\Lib\\site-packages\\biotite\\application\\muscle\\muscle-5.0.1428\\binaries\\muscle." )
      9 app.start()
---> 10 app.join()
     11 alignment = app.get_alignment()
     12 print(alignment)

~\anaconda3\lib\site-packages\biotite\application\application.py in wrapper(*args, **kwargs)
     56                     f"but {app_state} state is required"
     57                 )
---> 58             return func(*args, **kwargs)
     59         return wrapper
     60     return decorator

~\anaconda3\lib\site-packages\biotite\application\localapp.py in join(self, timeout)
    237 
    238         try:
--> 239             self.evaluate()
    240         except AppStateError:
    241             raise

~\anaconda3\lib\site-packages\biotite\application\muscle\app.py in evaluate(self)
     91 
     92     def evaluate(self):
---> 93         super().evaluate()
     94 
     95         newick = self._out_tree1_file.read().replace("\n", "")

~\anaconda3\lib\site-packages\biotite\application\msaapp.py in evaluate(self)
    159 
    160     def evaluate(self):
--> 161         super().evaluate()
    162         alignment_file = FastaFile.read(self._out_file)
    163         seq_dict = OrderedDict(alignment_file)

~\anaconda3\lib\site-packages\biotite\application\localapp.py in evaluate(self)
    258         if exit_code != 0:
    259             err_msg = self.get_stderr().replace("\n", " ")
--> 260             raise SubprocessError(
    261                 f"'{self._bin_path}' returned with exit code {exit_code}: "
    262                 f"{err_msg}"


SubprocessError: 'C:\Users\Work\anaconda3\Lib\site-packages\biotite\application\muscle\muscle-5.0.1428\binaries\muscle.' returned with exit code 1:   Invalid command line Unknown option in  

[padix-key]

Hi, is there something missing at the end of the log, as it finishes with Invalid command line Unknown option in? I just tested the snippet under Linux (with adapted binary path) and it works as expected. I will also be able to test the snippet under Windows within the next few days. Is the period in muscle. at the end of your path correct?

[kerbychok]

Hi,
thanks for the quick reply. I copied the whole log from the jupyter notebook using Anaconda and it ended with Invalid command line Unknown option in . I could not find anything after that.

If it helps, my anaconda is running on python 3.9.7.

For the muscle application, I have tried the 'muscle.exe' and 'muscle' binary path located in the unpacked zip file downloaded from the muscle website https://github.com/rcedgar/muscle/releases/tag/v5.0.1428. Both gave me the same result. Using the muscle.exe binary with powershell worked as expected, so I don't think there is any problem with the muscle program. I have also tried changing the directory of the MUSCLE binary to avoid typos but i still have the same problem.

Here is the snipet with the 'muscle.exe' and the following error log:

import biotite.application.muscle as muscle
import biotite.sequence as seq

seq1 = seq.ProteinSequence("BIQTITE")
seq2 = seq.ProteinSequence("TITANITE")
seq3 = seq.ProteinSequence("BISMITE")
seq4 = seq.ProteinSequence("IQLITE")
app = muscle.MuscleApp(sequences = [seq1, seq2, seq3, seq4], bin_path = "C:/Users/Kerby/Downloads/muscle-5.0.1428/binaries/muscle.exe")
app.start()
app.join()
alignment = app.get_alignment()
print(alignment) 

`

---------------------------------------------------------------------------
SubprocessError                           Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_4932/549366281.py in <module>
      8 app = muscle.MuscleApp(sequences = [seq1, seq2, seq3, seq4], bin_path = "C:/Users/Kerby/Downloads/muscle-5.0.1428/binaries/muscle.exe")
      9 app.start()
---> 10 app.join()
     11 alignment = app.get_alignment()
     12 print(alignment)

~\anaconda3\lib\site-packages\biotite\application\application.py in wrapper(*args, **kwargs)
     56                     f"but {app_state} state is required"
     57                 )
---> 58             return func(*args, **kwargs)
     59         return wrapper
     60     return decorator

~\anaconda3\lib\site-packages\biotite\application\localapp.py in join(self, timeout)
    237 
    238         try:
--> 239             self.evaluate()
    240         except AppStateError:
    241             raise

~\anaconda3\lib\site-packages\biotite\application\muscle\app.py in evaluate(self)
     91 
     92     def evaluate(self):
---> 93         super().evaluate()
     94 
     95         newick = self._out_tree1_file.read().replace("\n", "")

~\anaconda3\lib\site-packages\biotite\application\msaapp.py in evaluate(self)
    159 
    160     def evaluate(self):
--> 161         super().evaluate()
    162         alignment_file = FastaFile.read(self._out_file)
    163         seq_dict = OrderedDict(alignment_file)

~\anaconda3\lib\site-packages\biotite\application\localapp.py in evaluate(self)
    258         if exit_code != 0:
    259             err_msg = self.get_stderr().replace("\n", " ")
--> 260             raise SubprocessError(
    261                 f"'{self._bin_path}' returned with exit code {exit_code}: "
    262                 f"{err_msg}"

SubprocessError: 'C:/Users/Kerby/Downloads/muscle-5.0.1428/binaries/muscle.exe' returned with exit code 1:   Invalid command line Unknown option in `

Could there be an incompatibility with Jupyter notebook?

I could also try to place the muscle binary in the default path. But I don't know where the default path is located :/

[padix-key]

I forgot about your issue, I am sorry for that. It is probably too late for you by now, but I found the solution: Muscle version 5 is a complete rewrite of the software with new CLI arguments. Hence, invalid command line Unknown option in should be read as invalid command line Unknown option 'in', since also the argument for the input FASTA file changed. Since I worked with the old version of Muscle I was not able to reproduce your problem. With PR #373, this issue should be solved now: It provides to Application subclasses, one for the original Muscle 3 and a new one for Muscle 5.