Merge pull request #73 from zprobot/master

update: ibaqpy
bigbio · Nov 22, 2024 · 96892e6 · 96892e6
2 parents ad8efaa + 72090ff
commit 96892e6
Show file tree

Hide file tree

Showing 5 changed files with 12 additions and 12 deletions.
diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,5 @@ venv
 /tests/PXD003947/PXD003947-ibaq-norm.csv
 /tests/PXD003947/PXD003947-peptides-norm.csv
 /tests/PXD003947/PXD003947-peptides-norm.parquet
+/build/
+/dist/
diff --git a/ibaqpy/ibaq/ibaqpy_commons.py b/ibaqpy/ibaq/ibaqpy_commons.py
@@ -6,12 +6,10 @@
 from matplotlib import pyplot as plt
 
 PARQUET_COLUMNS = [
-    "protein_accessions",
+    "pg_accessions",
     "peptidoform",
     "sequence",
-    "charge",
-    "fragment_ion",
-    "isotope_label_type",
+    "precursor_charge",
     "channel",
     "condition",
     "biological_replicate",
@@ -52,12 +50,12 @@
 IBAQ_PPB = "IbaqPpb"
 
 parquet_map = {
-    "protein_accessions": PROTEIN_NAME,
+    "pg_accessions": PROTEIN_NAME,
     "peptidoform": PEPTIDE_SEQUENCE,
     "sequence": PEPTIDE_CANONICAL,
-    "charge": PEPTIDE_CHARGE,
-    "fragment_ion": FRAGMENT_ION,
-    "isotope_label_type": ISOTOPE_LABEL_TYPE,
+    "precursor_charge": PEPTIDE_CHARGE,
+    #"fragment_ion": FRAGMENT_ION,
+    #"isotope_label_type": ISOTOPE_LABEL_TYPE,
     "channel": CHANNEL,
     "condition": CONDITION,
     "biological_replicate": BIOREPLICATE,

diff --git a/ibaqpy/ibaq/peptide_normalization.py b/ibaqpy/ibaq/peptide_normalization.py
@@ -439,9 +439,9 @@ def get_unique_labels(self):
         return: A list of labels.
         """
         unique = self.parquet_db.sql(
-            "SELECT DISTINCT isotope_label_type FROM parquet_db"
+            "SELECT DISTINCT channel FROM parquet_db"
         ).df()
-        return unique["isotope_label_type"].tolist()
+        return unique["channel"].tolist()
 
     def get_unique_tec_reps(self):
         """

diff --git a/ibaqpy/ibaq/utils.py b/ibaqpy/ibaq/utils.py
@@ -10,7 +10,7 @@
 from sklearn.decomposition import PCA
 from sklearn.impute import KNNImputer
 
-from combat.pycombat import pycombat
+#from combat.pycombat import pycombat
 
 logging.basicConfig(
     format="%(asctime)s [%(funcName)s] - %(message)s", level=logging.DEBUG

diff --git a/setup.py b/setup.py
@@ -37,7 +37,7 @@ def readme():
         "qnorm",
         "seaborn",
         "typing_extensions",
-        "combat",
+        #"combat",
     ],
     entry_points={"console_scripts": ["ibaqpy=ibaqpy.ibaqpyc:main"]},
     classifiers=[