Handling ambiguous codons

[harika-shiats]

when i run the following viz.plot_ca_aa_freq_aa(in_file, 11,) I get the following error
TypeError Traceback (most recent call last)
Cell In[39], line 4
2 import pandas as pd
3 in_file = "C:/Users/aravi/Desktop/codonU/At/At_CKX_Prot.txt"
----> 4 viz.plot_ca_aa_freq_gene(in_file, 11,scale =str, min_len_threshold=66, n_components=2,organism_name= "Arabidopsis thaliana", save_image= True, folder_path= "C:/Users/aravi/Desktop/codonU/At" )

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\CodonU\vizualizer\plot_ca_aa_freq_gene.py:31, in plot_ca_aa_freq_gene(handle, genetic_table_num, scale, min_len_threshold, n_components, organism_name, save_image, folder_path)
29 cont_table.replace(0, 0.000001, inplace=True)
30 ca = ca_aa(cont_table, n_components)
---> 31 genes = ca.row_coordinates(cont_table)
33 if scale == 'aroma':
34 color_bar = [ProteinAnalysis(str(prot.seq)).aromaticity() for prot in
35 filter_reference(parse(handle, 'fasta'), min_len_threshold, 'aa')]

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\prince\utils.py:28, in check_is_dataframe_input..wrapper(*args, **kwargs)
24 if not isinstance(X, pd.DataFrame):
25 raise ValueError(
26 f"The X argument must be a pandas DataFrame, but got {type(X).name}"
27 )
---> 28 return func(*args, **kwargs)

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\prince\ca.py:19, in select_active_columns..impl(self, X, *method_args, **method_kwargs)
16 @functools.wraps(method)
17 def impl(self, X=None, *method_args, **method_kwargs):
18 if hasattr(self, "active_cols") and isinstance(X, pd.DataFrame):
---> 19 return method(self, X[self.active_cols], *method_args, **method_kwargs)
20 return method(self, X, *method_args, **method_kwargs)

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\prince\ca.py:159, in CA.row_coordinates(self, X)
155 else:
156 X = X / X.sum(axis=1)
158 return pd.DataFrame(
--> 159 data=X @ sparse.diags(self.col_masses_.to_numpy() ** -0.5) @ self.svd_.V.T,
160 index=pd.Index(row_names, name=index_name),
161 )

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_base.py:636, in spmatrix.rmatmul(self, other)
633 if isscalarlike(other):
634 raise ValueError("Scalar operands are not allowed, "
635 "use '*' instead")
--> 636 return self._rmul_dispatch(other)

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_base.py:614, in spmatrix._rmul_dispatch(self, other)
612 except AttributeError:
613 tr = np.asarray(other).transpose()
--> 614 ret = self.transpose()._mul_dispatch(tr)
615 if ret is NotImplemented:
616 return NotImplemented

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_base.py:532, in spmatrix._mul_dispatch(self, other)
530 return self._mul_vector(other.ravel()).reshape(M, 1)
531 elif other.ndim == 2 and other.shape[0] == N:
--> 532 return self._mul_multivector(other)
534 if isscalarlike(other):
535 # scalar value
536 return self._mul_scalar(other)

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_base.py:600, in spmatrix._mul_multivector(self, other)
599 def _mul_multivector(self, other):
--> 600 return self.tocsr()._mul_multivector(other)

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_compressed.py:498, in _cs_matrix._mul_multivector(self, other)
494 M, N = self.shape
495 n_vecs = other.shape[1] # number of column vectors
497 result = np.zeros((M, n_vecs),
--> 498 dtype=upcast_char(self.dtype.char, other.dtype.char))
500 # csr_matvecs or csc_matvecs
501 fn = getattr(_sparsetools, self.format + '_matvecs')

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_sputils.py:61, in upcast_char(*args)
59 if t is not None:
60 return t
---> 61 t = upcast(*map(np.dtype, args))
62 _upcast_memo[args] = t
63 return t

File ~\AppData\Local\Programs\Python\Python311\Lib\site-packages\scipy\sparse_sputils.py:53, in upcast(*args)
50 _upcast_memo[hash(args)] = t
51 return t
---> 53 raise TypeError('no supported conversion for types: %r' % (args,))

TypeError: no supported conversion for types: (dtype('float64'), dtype('O'))

kindly, let me know how to resolve this.

[SouradiptoC]

Can you check if the infile you are providing is in .fasta format and have no ambiguous codons?

[harika-shiats]

The file is in .txt format and it has ambiguous codons in it

[harika-shiats]

I'm using the below attached file for the analysis. I changed the .txt file to .fasta format. still getting the same error. I'm not able to attach this file in github since it is in .fasta file.

…

On Fri, Dec 6, 2024 at 8:41 AM Souradipto Choudhuri < ***@***.***> wrote: Can you check if the infile you are providing is in .fasta format and have no ambiguous codons? — Reply to this email directly, view it on GitHub <#9 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGCXHUQ26GCLW455ZDSLM7L2EEIVHAVCNFSM6AAAAABS722RIKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMRSGAZDQNBZGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[SouradiptoC]

I'm sorry mate, CodonU is not compatible with ambiguous codons...

[SouradiptoC]

If you want to have this functionality, please state the use cases and expected results for handling ambiguous codons