FunVIP 0.3.23.3__tar.gz → 0.3.23.5__tar.gz

{funvip-0.3.23.3 → funvip-0.3.23.5}/FunVIP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.23.3
+Version: 0.3.23.5
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0

{funvip-0.3.23.3 → funvip-0.3.23.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: FunVIP
-Version: 0.3.23.3
+Version: 0.3.23.5
 Summary: Fungal Validation & Identification Pipeline
 Author-email: Changwan Seo <wan101010@snu.ac.kr>
 License: GPL-3.0

{funvip-0.3.23.3 → funvip-0.3.23.5}/funvip/src/concatenate.py

@@ -155,7 +155,30 @@ def concatenate_df(V, path, opt):
         # Leave non-empty dataframes
         if isinstance(V.dict_gene_SR[gene], pd.DataFrame):
             gene_list.append(gene)
+
             df = deepcopy(V.dict_gene_SR[gene].set_index(["qseqid", "sseqid"]))
+
+            """
+            df = deepcopy(
+                V.dict_gene_SR[gene]
+                .set_index(["qseqid", "sseqid"])
+                .drop(
+                    columns=[
+                        "pident",
+                        "length",
+                        "mismatch",
+                        "gaps",
+                        "qstart",
+                        "qend",
+                        "sstart",
+                        "send",
+                        "evalue",
+                        "bitscore",
+                        "subject_group",
+                    ]
+                )
+            )
+            """
             df_list.append(df)
 
     if len(df_list) <= 0:
@@ -179,6 +202,7 @@ def concatenate_df(V, path, opt):
         df_multigene_regression_ori = pd.concat(df_list, axis=1)
 
         # Drop unnecessary columns for processing
+
         df_multigene_regression_ori.drop(
             columns=[
                 "pident",

{funvip-0.3.23.3 → funvip-0.3.23.5}/funvip/src/search.py

@@ -88,6 +88,7 @@ def merge_fragments(df) -> pd.DataFrame():
     # mismatch, gaps, and bitscore were calculated as sum of fragments
     # evalues were calculated by multiplying them, because they are probability
 
+    """
     df = df.groupby(["qseqid", "sseqid"], dropna=True, as_index=False).aggregate(
         {
             "qseqid": lambda x: set(x),
@@ -104,6 +105,24 @@ def merge_fragments(df) -> pd.DataFrame():
             "bitscore": np.sum,
         }
     )
+    """
+    # This part should be tested, especially in previous versions
+    df = df.groupby(["qseqid", "sseqid"], dropna=True, as_index=False).aggregate(
+        {
+            "qseqid": lambda x: set(x),
+            "sseqid": lambda x: set(x),
+            "pident": lambda x: tuple(x),
+            "length": lambda x: tuple(x),
+            "mismatch": "sum",
+            "gaps": "sum",
+            "qstart": lambda x: tuple(x),
+            "qend": lambda x: tuple(x),
+            "sstart": lambda x: tuple(x),
+            "send": lambda x: tuple(x),
+            "evalue": "prod",
+            "bitscore": "sum",
+        }
+    )
 
     # Calculate pident
     df["pident"] = df.apply(calculate_pident, axis=1)

{funvip-0.3.23.3 → funvip-0.3.23.5}/funvip/src/validate_input.py

@@ -70,9 +70,9 @@ class Funinfo:
         if gene in self.seq:
             error = f"In {self.source}, More than 1 sequence for {gene} found for {self.id} during update_seqrecord"
         elif gene is None:
-            self.unclassified_seq.append(str(seq.seq.ungap("-")))
+            self.unclassified_seq.append(str(seq.seq).replace("-", ""))
         else:
-            self.seq[gene] = str(seq.seq.ungap("-"))
+            self.seq[gene] = str(seq.seq).replace("-", "")
 
         self.bygene_species[gene] = self.ori_species
 

{funvip-0.3.23.3 → funvip-0.3.23.5}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "FunVIP"
-version = "0.3.23.3"
+version = "0.3.23.5"
 description = "Fungal Validation & Identification Pipeline"
 authors = [{name = "Changwan Seo", email = "wan101010@snu.ac.kr"}]
 urls = { "Homepage" = "https://github.com/Changwanseo/FunVIP" }