Merge pull request #146 from faridrashidi/develop

version 0.2.3

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.2
+current_version = 0.2.3
 commit = True
 message = [skip ci] {current_version} → {new_version}
 tag = False

README.rst

@@ -20,11 +20,6 @@ Trisicell utilizes expressed SNVs and Indels to infer evolutionary
 relationships between genomic alterations and the cells that harbor them.
 
 
-Manuscript
-----------
-Please see our `preprint`_ on **bioRxiv** to learn more.
-
-
 Support
 -------
 Feel free to submit an `issue <https://github.com/faridrashidi/trisicell/issues/new/choose>`_.

setup.py

@@ -12,7 +12,7 @@
     __author__ = ", ".join(["Farid Rashidi"])
     __maintainer__ = ", ".join(["Farid Rashidi"])
     __email__ = ", ".join(["[email protected]"])
-    __version__ = "0.2.2"
+    __version__ = "0.2.3"
 
 if platform == "linux" or platform == "linux2":
     os.environ["CC"] = "g++"

trisicell/__init__.py

@@ -7,5 +7,5 @@
 __author__ = ", ".join(["Farid Rashidi"])
 __maintainer__ = ", ".join(["Farid Rashidi"])
 __email__ = ", ".join(["[email protected]"])
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 __all__ = (datasets, io, logg, pl, pp, settings, tl, ul)

trisicell/io/_genotype.py

@@ -18,7 +18,7 @@ def read(filepath):
     ----------
     filepath : :obj:`str`
         The path to the file. The extension must be one of
-        [`.SC`, `.CFMatrix`, `.h5ad`, `.h5ad.gz`, `.nwk`]
+        [`.tsv`, `.SC`, `.CFMatrix`, `.h5ad`, `.h5ad.gz`, `.nwk`]
 
     Returns
     -------

trisicell/tl/solver/booster/_booster.py

@@ -91,6 +91,7 @@ def booster(
         sample_size = int(dep_weight * (n_muts**2) / (sample_size**2))
 
     detail = {}
+    df_input.index.name = "cellIDxmutID"
 
     s_time = time.time()
     # subsampling matrices and solving them

trisicell/tl/solver/booster/_subsamples.py

@@ -19,7 +19,6 @@ def subsampling(
     tmpdir,
     disable_tqdm,
 ):
-
     if solver.lower() == "scite":
         time_limit = n_iterations
 
@@ -29,6 +28,8 @@ def run(i):
             dfn = df_input.sample(n=sample_size, replace=False, axis=1)
         elif sample_on == "cells":
             dfn = df_input.sample(n=sample_size, replace=False, axis=0)
+        else:
+            tsc.logg.error("`sample_on` must be either 'muts' or 'cells'!")
 
         if solver.lower() == "phiscs":
             dfo = tsc.tl.phiscsb(dfn, alpha, beta, experiment=True)
@@ -45,6 +46,8 @@ def run(i):
                 return None
             dfo, _ = tsc.tl.scistree(dfn, alpha, beta, experiment=True)
             dfo.to_csv(f"{tmpdir}/{i}.CFMatrix", sep="\t")
+        else:
+            tsc.logg.error("`solver` must be either 'phiscs' or 'scite'!")
 
     with tsc.ul.tqdm_joblib(
         tqdm(