newick tree is not generating for CRC data
CSTE7007 opened this issue · comments
I ran the code for example data and that produced four files as below:
data/sample/overview_B.csv
data/sample/overview_tree.dot
data/sample/overview_tree.newick
data/sample/overview_tree_without_cells.dot
where overview_tree.newick
file had values inside.
But when I ran the code for data/CRC
folder as follow:
python src/condor.py -i data/CRC/input/character_matrix.csv -a 0.0018 -b 0.001 -k 1 -r data/CRC/input/total_readcounts.csv -v data/CRC/input/alt_readcounts.csv -o data/CRC/CRC
it generated
data/CRC/CRC_B.csv
data/CRC/CRC_tree.dot
data/CRC/CRC_tree.newick
data/CRC/CRC_tree_without_cells.dot
But the data/CRC/CRC_tree.newick
file was with empty value as ();
Thank you for your interest in using ConDoR. I have now fixed the code so it should output the newick file correctly (before this change, the cell name had to start with 's' for the newick file to be generated correctly). I have tested that the code works now, but please let me know if the problem persists.