From b984ca39470e7352ac79e28d62753757f9247581 Mon Sep 17 00:00:00 2001
From: Vasudha Jha <reachvasudha27@gmail.com>
Date: Mon, 24 Jul 2023 10:26:54 -0700
Subject: [PATCH] add additional requirements from genotype

---
 genomap/genotype/genotype.py | 17 +++--------------
 requirements.txt             |  2 ++
 2 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/genomap/genotype/genotype.py b/genomap/genotype/genotype.py
index e723bd5..3442b3f 100644
--- 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
index 407aff0..6e6e41d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -5,9 +5,11 @@ keras
 lime
 louvain
 numpy
+openpyxl
 pandas
 phate
 pot
+pybiomart
 scanpy
 scanorama
 scipy