From 72090ff96856ba525f9acb0e88f9a49e23ddce6d Mon Sep 17 00:00:00 2001
From: zprobot <1727697083@qq.com>
Date: Thu, 31 Oct 2024 16:59:18 +0800
Subject: [PATCH] update: ibaqpy

---
 .gitignore                           |  2 ++
 ibaqpy/ibaq/ibaqpy_commons.py        | 14 ++++++--------
 ibaqpy/ibaq/peptide_normalization.py |  4 ++--
 ibaqpy/ibaq/utils.py                 |  2 +-
 setup.py                             |  2 +-
 5 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/.gitignore b/.gitignore
index 9f404e4..ed58c0e 100644
--- 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/
\ No newline at end of file
diff --git a/ibaqpy/ibaq/ibaqpy_commons.py b/ibaqpy/ibaq/ibaqpy_commons.py
index 2dd2337..d77a391 100644
--- 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
index aaf6029..f24fbf3 100644
--- 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
index 310c1ab..f9cecc1 100644
--- 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
index 470ec63..2728ced 100644
--- 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=[