Fix write_gct too much strip

pycytominer/__init__.py

@@ -9,4 +9,3 @@
 from .normalize import normalize
 from .sparse_random_projection import sparse_random_projection
 from .variance_threshold import variance_threshold
-from .write_gct import write_gct

pycytominer/cyto_utils/__init__.py

@@ -20,3 +20,4 @@
     Whiten,
     RobustMAD,
 )
+from .write_gct import write_gct

pycytominer/write_gct.py → pycytominer/cyto_utils/write_gct.py

@@ -10,7 +10,7 @@
 import csv
 import numpy as np
 import pandas as pd
-from pycytominer.cyto_utils.features import infer_cp_features
+from pycytominer.cyto_utils import infer_cp_features
 
 
 def write_gct(
@@ -60,7 +60,7 @@ def write_gct(
         .rename({"index": "id"}, axis="columns")
         .transpose()
     )
-    metadata_part.index = metadata_part.index.str.lstrip("Metadata_")
+    metadata_part.index = [x.replace("Metadata_", "") for x in metadata_part.index]
 
     nrow_feature, ncol_features = feature_df.shape
     _, ncol_metadata = metadata_df.shape

pycytominer/tests/test_write_gct.py → pycytominer/tests/test_cyto_utils/test_write_gct.py

@@ -3,14 +3,15 @@
 import tempfile
 import pytest
 import pandas as pd
-from pycytominer import write_gct
+from pycytominer.cyto_utils import write_gct
 
 # Build data to use in tests
 data_replicate_df = pd.concat(
     [
         pd.DataFrame(
             {
                 "Metadata_g": "a",
+                "Metadata_t": "t",
                 "Cells_x": [1, 1, -1],
                 "Cytoplasm_y": [5, 5, -5],
                 "Nuclei_z": [2, 2, -2],
@@ -19,6 +20,7 @@
         pd.DataFrame(
             {
                 "Metadata_g": "b",
+                "Metadata_t": "u",
                 "Cells_x": [1, 3, 5],
                 "Cytoplasm_y": [8, 3, 1],
                 "Nuclei_z": [5, -2, 1],
@@ -59,7 +61,7 @@ def test_write_gct():
             gct_row_list.append(row)
 
     assert gct_row_list[0] == ["#1.3"]
-    assert gct_row_list[1] == ["3", "6", "1", "2"]
+    assert gct_row_list[1] == ["3", "6", "1", "3"]
     assert gct_row_list[2] == [
         "id",
         "cp_feature_name",
@@ -71,9 +73,10 @@ def test_write_gct():
         "SAMPLE_5",
     ]
     assert gct_row_list[3] == ["g", "nan", "a", "a", "a", "b", "b", "b"]
-    assert gct_row_list[4] == ["h", "nan", "c", "c", "c", "d", "d", "d"]
-    assert gct_row_list[5] == ["Cells_x", "Cells_x", "1", "1", "-1", "1", "3", "5"]
-    assert gct_row_list[6] == [
+    assert gct_row_list[4] == ["t", "nan", "t", "t", "t", "u", "u", "u"]
+    assert gct_row_list[5] == ["h", "nan", "c", "c", "c", "d", "d", "d"]
+    assert gct_row_list[6] == ["Cells_x", "Cells_x", "1", "1", "-1", "1", "3", "5"]
+    assert gct_row_list[7] == [
         "Cytoplasm_y",
         "Cytoplasm_y",
         "5",
@@ -83,7 +86,7 @@ def test_write_gct():
         "3",
         "1",
     ]
-    assert gct_row_list[7] == ["Nuclei_z", "Nuclei_z", "2", "2", "-2", "5", "-2", "1"]
+    assert gct_row_list[8] == ["Nuclei_z", "Nuclei_z", "2", "2", "-2", "5", "-2", "1"]
 
 
 def test_write_gct_infer_features():
@@ -131,7 +134,7 @@ def test_write_gct_with_feature_metadata():
             "id": ["color", "shape"],
             "Cells_x": ["blue", "triangle"],
             "Cytoplasm_y": ["red", "square"],
-            "Nuclei_z": ["green", "oval"]
+            "Nuclei_z": ["green", "oval"],
         }
     ).transpose()
 
@@ -150,7 +153,7 @@ def test_write_gct_with_feature_metadata():
             gct_row_list.append(row)
 
     assert gct_row_list[0] == ["#1.3"]
-    assert gct_row_list[1] == ["3", "6", "2", "2"]
+    assert gct_row_list[1] == ["3", "6", "2", "3"]
     assert gct_row_list[2] == [
         "id",
         "color",
@@ -163,10 +166,41 @@ def test_write_gct_with_feature_metadata():
         "SAMPLE_5",
     ]
     assert gct_row_list[3] == ["g", "nan", "nan", "a", "a", "a", "b", "b", "b"]
-    assert gct_row_list[4] == ["h", "nan", "nan", "c", "c", "c", "d", "d", "d"]
-    assert gct_row_list[5] == ["Cells_x", "blue", "triangle", "1", "1", "-1", "1", "3", "5"]
-    assert gct_row_list[6] == ["Cytoplasm_y", "red", "square", "5", "5", "-5", "8", "3", "1"]
-    assert gct_row_list[7] == ["Nuclei_z", "green", "oval", "2", "2", "-2", "5", "-2", "1"]
+    assert gct_row_list[4] == ["t", "nan", "nan", "t", "t", "t", "u", "u", "u"]
+    assert gct_row_list[5] == ["h", "nan", "nan", "c", "c", "c", "d", "d", "d"]
+    assert gct_row_list[6] == [
+        "Cells_x",
+        "blue",
+        "triangle",
+        "1",
+        "1",
+        "-1",
+        "1",
+        "3",
+        "5",
+    ]
+    assert gct_row_list[7] == [
+        "Cytoplasm_y",
+        "red",
+        "square",
+        "5",
+        "5",
+        "-5",
+        "8",
+        "3",
+        "1",
+    ]
+    assert gct_row_list[8] == [
+        "Nuclei_z",
+        "green",
+        "oval",
+        "2",
+        "2",
+        "-2",
+        "5",
+        "-2",
+        "1",
+    ]
 
 
 def test_write_gct_assert_error():
@@ -176,7 +210,7 @@ def test_write_gct_assert_error():
             {
                 "Cells_x": ["blue", "triangle"],
                 "Cytoplasm_y": ["red", "square"],
-                "Nuclei_z": ["green", "oval"]
+                "Nuclei_z": ["green", "oval"],
             }
         ).transpose()
 
@@ -188,4 +222,4 @@ def test_write_gct_assert_error():
             feature_metadata=feature_metadata,
             version="#1.3",
         )
-    assert "make sure feature metadata has row named 'id'" in str(ae.value)
+    assert "make sure feature metadata has row named 'id'" in str(ae.value)