Can't graph a multiple alignment

[rpestana94]

I'm trying to use biotite to graph multiple alignments but I always get the same error:

graphics.plot_sequence_logo(ax, alignment)
File "/home/arcadio/anaconda3/envs/py38/lib/python3.8/site-packages/biotite/sequence/graphics/logo.py", line 87, in plot_sequence_logo
ha="left", va="bottom", color=colors[j],
IndexError: list index out of range

The file test_few_sample.fasta has 13 sequences, each one about 1270 amino acids length.

import biotite.sequence as seq
import biotite.sequence.io.fasta as fasta
import biotite.sequence.graphics as graphics
import biotite.sequence.align as align
import matplotlib.pyplot as plt

fasta_file = fasta.FastaFile.read("test_few_sample.fasta")
all_sequences = fasta.get_sequences(fasta_file)

ids = []
sequences = []

for header, seq_str in fasta_file.items():
    identifier = header.split("|")[-1].split()[0].split(":")[0]
    ids.append(identifier)
    sequences.append(seq.ProteinSequence(seq_str))

matrix = align.SubstitutionMatrix.std_protein_matrix()
alignment, order, tree, distances = align.align_multiple(
    sequences, matrix, gap_penalty=(-10,-1), terminal_penalty=False
)

alignment = alignment[:, order]
ids = [ids[i] for i in order]

fig = plt.figure(figsize=(8.0, 3.0))
ax = fig.add_subplot(111)
graphics.plot_sequence_logo(ax, alignment)
ax.set_xticks([5,10,15,20])
ax.set_xlabel("Residue position")
ax.set_ylabel("Bits")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
fig.tight_layout()

plt.show()

I don't know where is the error, any help is appreciated.

[padix-key]

You stumbled upon a bug in the color scheme generation, thank you for the report. I will prepare a fix for the next release.
The reason is, that at least one of you protein sequences contains either an 'X' or a '*'.
For now, there are two ways for you to fix this:

1. If the sequence contains '*': These symbols probably do not convey information in the plot. So you can remove them via the remove_stops() method. In the context of your code this means: sequences.append(seq.ProteinSequence(seq_str).remove_stops()).
2. Otherwise you can fix the line that produces this bug directly in your Biotite installation: Go to

   biotite/src/biotite/sequence/graphics/colorschemes.py

   Line 46 in 723c09b

   colors = [None] * len(scheme["colors"])

   and replace len(scheme["colors"]) with len(alphabet).

[rpestana94]

Thanks, I used the second approach and works perfect