Giters

raphael-group / ConDoR

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

newick tree is not generating for CRC data

CSTE7007 opened this issue · comments

commented

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 ();

commented

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.