Remove unused Python dependencies

Author: kevinlul

Dockerfile

@@ -30,8 +30,8 @@ RUN curl -LO https://jbrowse.org/releases/JBrowse-${JBROWSE_VERSION}/JBrowse-${J
     mv JBrowse-${JBROWSE_VERSION} /var/www/html/jbrowse && \
     rm JBrowse-${JBROWSE_VERSION}.zip && \
     cd /var/www/html/jbrowse && ./setup.sh
-RUN pip install --no-cache-dir numpy==1.11.2 pymongo==3.8.0 requests==2.22.0 && \
-    pip3 install --no-cache-dir numpy==1.17.2 pymongo==3.8.0 requests==2.20.0 Jinja2==2.10.1
+RUN pip install --no-cache-dir pymongo==3.8.0 requests==2.22.0 && \
+    pip3 install --no-cache-dir pymongo==3.8.0 requests==2.20.0 Jinja2==3.1.2
 COPY config-template /var/www/html/config
 WORKDIR /var/www/html
 CMD service mongodb start && exec apache2-foreground

src/guide-finder/core/cfd_code/cfd_score_calculator3.py

@@ -2,14 +2,14 @@
 
 #Calculates the Cutting Frequency Determination score
 #Requirements: 1. Pickle file with mismatch scores in working directory
-#              2. Pickle file containing PAM scores in working directory 
+#              2. Pickle file containing PAM scores in working directory
 #Input: 1. 23mer WT sgRNA sequence
 #       2. 23mer Off-target sgRNA sequence
 #Output: CFD score
 import pickle
 import argparse
 import re
-import numpy as np
+
 
 import os
 dir_path = os.path.dirname(os.path.abspath(__file__))
@@ -37,7 +37,7 @@ def get_mm_pam_scores():
         mm_scores = pickle.load(open(os.path.join(dir_path,'mismatch_score.pkl'),'rb'))
         pam_scores = pickle.load(open(os.path.join(dir_path,'pam_scores.pkl'),'rb'))
         return (mm_scores,pam_scores)
-    except Exception as e: 
+    except Exception as e:
         raise Exception("Could not find file with mismatch scores or PAM scores")
 
 #Calculates CFD score