Newick tree file with new lines

[bburkhar1]

Greetings,

I'm using MAFFT to output Newick Tree files for my sequences, but MAFFT seems to output the Newick files with multiple new lines / carriage returns and TreeCluster seems to choke on it (see traceback below). My only work around is to open the raw Newick output and use find and replace to re-organize the file so everything is on one line (rather than many lines by deleting the returns). I don't know if this was intended but it seems like it would be better a beginner (like me) if one could go straight from the MAFFT tree output into TreeCluster unless I'm making a mistake somewhere in TreeCluster (or MAFFT which I realize you don't support... but it is widely used in the field so I'd accept any suggestions). Thanks!

Traceback (most recent call last): File "/usr/local/lib/python3.10/dist-packages/treeswift/Tree.py", line 1443, in read_tree_newick while parse_label or ts[i] not in {':', ',', ';', ')', '['}: IndexError: string index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/local/bin/TreeCluster.py", line 605, in trees.append(read_tree_newick(l)) File "/usr/local/lib/python3.10/dist-packages/treeswift/Tree.py", line 1452, in read_tree_newick raise RuntimeError(f"Failed to parse string as Newick: {ts}") RuntimeError: Failed to parse string as Newick: 1_Sequence_0001

[niemasd]

Thank you for reaching out! Would you be able to attach the file it failed to load (or if it contains sensitive information, a similar example file that also triggers the issue)?

[bburkhar1]

Yes, here is an example. The first file is the initial Newick Tree output from MAFFT and it has the error (fail). The second file is the same except that I have removed the returns and it runs successfully. Newick_tree_fail.txt Newick_tree_success.txt

[niemasd]

Thanks! I think I've patched it in the most recent version of TreeSwift (the Python package that TreeCluster uses to parse/traverse trees). Can you try updating to TreeSwift v1.1.35 and see if that fixes the issue? E.g.

pip3 install --upgrade treeswift

[niemasd]

I think that should have fixed it, so I'll go ahead and close this GitHub Issue, but please feel free to reopen it if the issue persists even after updating TreeSwift

[bburkhar1]

Hi,

Thanks for the quick update. I updated TreeSwift to v1.1.35, but it gave another error (with the same file I shared previously) at a different line. See traceback below:

$ TreeCluster.py -i Newick_tree_fail.txt -o Tree_test.txt -t 0.7 -m max_clade Traceback (most recent call last): File "/home/bburkhar/.local/lib/python3.10/site-packages/treeswift/Tree.py", line 1454, in read_tree_newick while parse_label or ts[i] not in {':', ',', ';', ')', '['}: IndexError: string index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/usr/local/bin/TreeCluster.py", line 605, in trees.append(read_tree_newick(l)) File "/home/bburkhar/.local/lib/python3.10/site-packages/treeswift/Tree.py", line 1463, in read_tree_newick raise RuntimeError(f"Failed to parse string as Newick: {ts}") RuntimeError: Failed to parse string as Newick: 1_220921_0000252941

[niemasd]

Woops, thank you for catching that! I had incorrectly assumed that TreeCluster was just directly using TreeSwift's read_tree_newick function for reading the tree; I should have tested it more thoroughly 😄 I just patched TreeCluster's handling of reading Newick trees to use the aforementioned patch I implemented in TreeSwift. Thus, this issue should be fixed with TreeSwift v1.1.35 and TreeCluster v1.0.4:

pip3 install --upgrade treecluster treeswift

Try it out and let me know if it works for you now 😄

[bburkhar1]

It is working now. Thanks for the quick responses and clear instructions.!

[niemasd]

No problem at all! Thank you for reporting this bug!