add additional requirements from genotype

xinglab-ai · Jul 24, 2023 · b984ca3 · b984ca3
1 parent 20aac82
commit b984ca3
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Showing 2 changed files with 5 additions and 14 deletions.
diff --git a/genomap/genotype/genotype.py b/genomap/genotype/genotype.py
@@ -10,8 +10,9 @@
 import pandas as pd
 import numpy as np
 import scipy
-
-
+import openpyxl
+from pybiomart import Dataset
+import re
 
 def sctype_score(scRNAseqData, scaled=True, gs=None, gs2=None, gene_names_to_uppercase=True, cell_types=None):
     # Ensure input is a pandas DataFrame
@@ -82,11 +83,6 @@ def sctype_score(scRNAseqData, scaled=True, gs=None, gs2=None, gene_names_to_upp
 
     return es
 
-
-
-
-import openpyxl
-
 def gene_sets_prepare(path_to_db_file, cell_type):
     # Read the Excel file
     cell_markers = pd.read_excel(path_to_db_file, engine='openpyxl')
@@ -134,8 +130,6 @@ def process_genes(x):
 
     return {'gs_positive': gs, 'gs_negative': gs2, 'cell_types': cell_types}
 
-
-
 def correct_gene_symbols(gene_symbols, species="human"):
     if isinstance(gene_symbols, str):
         gene_symbols = gene_symbols.split(",")
@@ -161,11 +155,6 @@ def correct_gene_symbols(gene_symbols, species="human"):
         return ""
 
 
-
-
-from pybiomart import Dataset
-import re
-
 def check_gene_symbols(x, unmapped_as_na=True, map=None, species="human"):
     if species == "human":
         dataset_name = 'hsapiens_gene_ensembl'

diff --git a/requirements.txt b/requirements.txt
@@ -5,9 +5,11 @@ keras
 lime
 louvain
 numpy
+openpyxl
 pandas
 phate
 pot
+pybiomart
 scanpy
 scanorama
 scipy
-Original file line number
+Diff line change
@@ Expand Up / @@ -5,9 +5,11 @@ keras @@
     lime
     louvain
     numpy
+    openpyxl
     pandas
     phate
     pot
+    pybiomart
     scanpy
     scanorama
     scipy
@@ Expand Down @@