FunVIP 0.3.24.1__tar.gz → 0.3.24.2__tar.gz

{funvip-0.3.24.1 → funvip-0.3.24.2}/FunVIP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.24.1
+Version: 0.3.24.2
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0

{funvip-0.3.24.1 → funvip-0.3.24.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.24.1
+Version: 0.3.24.2
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0

{funvip-0.3.24.1 → funvip-0.3.24.2}/funvip/src/ext.py

@@ -310,6 +310,7 @@ def RAxML(
     bootstrap=100,
     partition=None,
     model="-m GTRGAMMA",
+    version="old",
 ):
     if model == "skip":
         model = ""
@@ -328,7 +329,15 @@ def RAxML(
     elif platform == "darwin":
         CMD = f"raxmlHPC-PTHREADS -s '{fasta}' -n '{out}' -p 1 -T {thread} -f a -# {bootstrap} -x 1 {model}"
     else:
-        CMD = f"raxmlHPC-PTHREADS-AVX -s '{fasta}' -n '{out}' -p 1 -T {thread} -f a -# {bootstrap} -x 1 {model}"
+        if version == "old":
+            CMD = f"raxmlHPC-PTHREADS-AVX -s '{fasta}' -n '{out}' -p 1 -T {thread} -f a -# {bootstrap} -x 1 {model}"
+        elif version == "new":
+            CMD = f"raxmlHPC-PTHREADS-AVX2 -s '{fasta}' -n '{out}' -p 1 -T {thread} -f a -# {bootstrap} -x 1 {model}"
+        else:
+            logging.error(
+                f"DEVELOPMENTAL ERROR - unexpected RAxML version, {version} in ext.py"
+            )
+            raise Exception
 
     if not (partition is None):
         CMD += f" -q {partition}"

{funvip-0.3.24.1 → funvip-0.3.24.2}/funvip/src/initialize.py

@@ -139,6 +139,9 @@ def check(
 # Use print instead of logging here, because logging has not been defined here
 class Path:
     def __init__(self, root):
+        # For RAxML updates
+        self.raxml_version = "old"
+
         # For universal data used in every run
         self.sys_path = os.path.abspath(f"{os.path.dirname(__file__)}/../")
 
@@ -174,7 +177,6 @@ class Path:
                 }
             else:
                 check_commands = {
-                    "RAxML": "raxmlHPC-PTHREADS-AVX -h",
                     "Modeltest-NG": "modeltest-ng --help",
                     "IQTREE": "iqtree -h",
                     "MMseqs2": "mmseqs -h",
@@ -192,6 +194,24 @@ class Path:
                     print(f"[ERROR] {program} not installed!")
                     install_flag = 1
 
+            # For RAxML, there are two versions
+            # I don't know why, but apt install RAxML can use raxmlHPC-PTHREADS-AVX,
+            # while conda install RAxML can use raxmlHPC -PTHREADS-AVX / raxmlHPC-PTHREADS-AVX2 (blank between raxmlHPC and -PTHREADS-AVX)
+            # However, if using 'raxmlHPC -PTHREADS-AVX', the computer cannot utilize full threads
+            return_code_1 = subprocess.call(
+                "raxmlHPC-PTHREADS-AVX -h", shell=True, stdout=open(os.devnull, "wb")
+            )
+            return_code_2 = subprocess.call(
+                "raxmlHPC-PTHREADS-AVX2 -h", shell=True, stdout=open(os.devnull, "wb")
+            )
+
+            if return_code_1 != 0 and return_code_2 != 0:
+                print(f"[ERROR] RAxML not installed!")
+                install_flag = 1
+
+            if return_code_2 == 0:
+                self.raxml_version = "new"
+
             if install_flag == 1:
                 if sys.platform == "darwin":
                     print(

{funvip-0.3.24.1 → funvip-0.3.24.2}/funvip/src/tree.py

@@ -90,6 +90,7 @@ def pipe_tree(V, path, opt, model_dict):
                         thread=opt.thread,
                         bootstrap=opt.bootstrap,
                         model=model_dict[group][gene],
+                        version=path.raxml_version,
                     )
 
                 elif opt.method.tree.lower() == "iqtree":
@@ -131,6 +132,7 @@ def pipe_tree(V, path, opt, model_dict):
                         bootstrap=opt.bootstrap,
                         partition=f"{path.out_alignment}/{opt.runname}_{group}.partition",
                         model=model_dict[group][gene],
+                        version=path.raxml_version,
                     )
 
                 elif opt.method.tree.lower() == "iqtree":

{funvip-0.3.24.1 → funvip-0.3.24.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "FunVIP"
-version = "0.3.24.1"
+version = "0.3.24.2"
 description = "Fungal Validation & Identification Pipeline"
 authors = [{name = "Changwan Seo", email = "wan101010@snu.ac.kr"}]
 urls = { "Homepage" = "https://github.com/Changwanseo/FunVIP" }