[bug report] Error of dealing with file extension when saving bpp file

[heqin-zhu]

Thank you for your excellent work on MXfold2! While using the tool to save bpp files, I encountered a bug: the line of code at the link below incorrectly splits the sequence name (header) in the FASTA file into a "name" and "extension", leading to truncated filenames for the output bpp files.

Link to the problematic code:

mxfold2/mxfold2/predict.py

Line 67 in 51b2136

fn = os.path.splitext(fn)[0]

For example, when processing the FASTA file tmp.fasta with the header:

>tmRNA_Xyle.fast._TRW-155920_1-355
AGUAUCUGUAGUCGUC

Running the command mxfold2 predict @./models/TrainSetAB.conf tmp.fasta --bpp . generates a bpp file named tmRNA_Xyle.fast.bpp (incorrectly truncated, missing the _TRW-155920_1-355 suffix) instead of using the full sequence name.

To resolve this issue, I recommend removing the aforementioned line of code, as it unnecessarily splits the sequence header and causes the filename truncation.