- refactored import check to shared function

- global in CORE formatting change
edilytics · Mar 29, 2024 · e9cabb9 · e9cabb9
1 parent 05104ae
commit e9cabb9
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Showing 10 changed files with 23 additions and 70 deletions.
diff --git a/CRISPResso2/CRISPRessoAggregateCORE.py b/CRISPResso2/CRISPRessoAggregateCORE.py
@@ -17,12 +17,6 @@
 import traceback
 from datetime import datetime
 from CRISPResso2 import CRISPRessoShared
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
-
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 from CRISPResso2.CRISPRessoMultiProcessing import get_max_processes, run_plot
 
@@ -79,7 +73,7 @@ def main():
 
         args = parser.parse_args()
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -14,11 +14,6 @@
 import traceback
 from datetime import datetime
 from CRISPResso2 import CRISPRessoShared
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
 from CRISPResso2 import CRISPRessoMultiProcessing
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 
@@ -120,7 +115,7 @@ def main():
 
         _jp = lambda filename: os.path.join(OUTPUT_DIRECTORY, filename) #handy function to put a file in the output directory
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -31,11 +31,11 @@
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 from CRISPResso2 import CRISPRessoShared
 
-try:
+if CRISPRessoShared.is_C2Pro_installed():
     from CRISPRessoPro import __version__ as CRISPRessoProVersion
-    pro_installed = True
-except:
-    pro_installed = False
+    C2PRO_INSTALLED = True
+else:
+    C2PRO_INSTALLED = False
 
 from CRISPResso2 import CRISPResso2Align
 from CRISPResso2 import CRISPRessoMultiProcessing
@@ -1172,7 +1172,7 @@ def print_stacktrace_if_debug():
             raise CRISPRessoShared.BadParameterException("Needleman Wunsch gap extend penalty must be <= 0")
 
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not C2PRO_INSTALLED:
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot
@@ -1677,7 +1677,7 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited
 
         #now that we're done with adding possible guides and amplicons, go through each amplicon and compute quantification windows
         info('Computing quantification windows', {'percent_complete': 2})
-        if pro_installed:
+        if C2PRO_INSTALLED:
             info(f'CRISPRessoPro v{CRISPRessoProVersion} installed', {'percent_complete': 3})
         else:
             info(f'CRISPRessoPro not installed', {'percent_complete': 3})
@@ -3675,7 +3675,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                     plot_2a_input = {
                         'nuc_pct_df': nuc_df_for_plot,
                         'mod_pct_df': mod_df_for_plot,
-                        'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and pro_installed else plot_root,
+                        'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
                         'save_also_png': save_png,
                         'sgRNA_intervals': sgRNA_intervals,
                         'sgRNA_names': sgRNA_names,
@@ -3723,7 +3723,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         plot_2b_input = {
                             'nuc_pct_df': nuc_df_for_plot.iloc[:, sel_cols],
                             'mod_pct_df': mod_df_for_plot.iloc[:, sel_cols],
-                            'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and pro_installed else plot_root,
+                            'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
                             'save_also_png': save_png,
                             'sgRNA_intervals': new_sgRNA_intervals,
                             'sgRNA_names': sgRNA_names,
@@ -4093,7 +4093,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                     plot_4g_input = {
                         'nuc_pct_df': hdr_nucleotide_percentage_summary_df,
                         'mod_pct_df': hdr_modification_percentage_summary_df,
-                        'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and pro_installed else plot_root,
+                        'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
                         'save_also_png': save_png,
                         'sgRNA_intervals': sgRNA_intervals,
                         'quantification_window_idxs': include_idxs_list,
@@ -4691,7 +4691,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                 plot_11a_input = {
                     'nuc_pct_df': pe_nucleotide_percentage_summary_df,
                     'mod_pct_df': pe_modification_percentage_summary_df,
-                    'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and pro_installed else plot_root,
+                    'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
                     'save_also_png': save_png,
                     'sgRNA_intervals': sgRNA_intervals,
                     'sgRNA_names': sgRNA_names,
@@ -4751,7 +4751,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                     plot_11b_input = {
                         'nuc_pct_df': pe_nucleotide_percentage_summary_df.iloc[:, sel_cols],
                         'mod_pct_df': pe_modification_percentage_summary_df.iloc[:, sel_cols],
-                        'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and pro_installed else plot_root,
+                        'fig_filename_root': f'{_jp(pro_output_name)}' if not args.use_matplotlib and C2PRO_INSTALLED else plot_root,
                         'save_also_png': save_png,
                         'sgRNA_intervals': new_sgRNA_intervals,
                         'sgRNA_names': sgRNA_names,

diff --git a/CRISPResso2/CRISPRessoCompareCORE.py b/CRISPResso2/CRISPRessoCompareCORE.py
@@ -10,11 +10,6 @@
 import traceback
 import argparse
 from CRISPResso2 import CRISPRessoShared
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 
 import logging
@@ -113,7 +108,7 @@ def main():
 
         args = parser.parse_args()
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/CRISPResso2/CRISPRessoMetaCORE.py b/CRISPResso2/CRISPRessoMetaCORE.py
@@ -13,11 +13,6 @@
 import traceback
 import json
 from CRISPResso2 import CRISPRessoShared
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
 from CRISPResso2 import CRISPRessoMultiProcessing
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 
@@ -100,7 +95,7 @@ def main():
 
         args = parser.parse_args()
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/CRISPResso2/CRISPRessoPooledCORE.py b/CRISPResso2/CRISPRessoPooledCORE.py
@@ -19,11 +19,7 @@
 from CRISPResso2 import CRISPRessoShared
 from CRISPResso2 import CRISPRessoMultiProcessing
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
+
 import traceback
 
 import logging
@@ -339,7 +335,7 @@ def main():
 
         args = parser.parse_args()
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/CRISPResso2/CRISPRessoShared.py b/CRISPResso2/CRISPRessoShared.py
@@ -24,12 +24,6 @@
 import logging
 from inspect import getmodule, stack
 
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
-
 from CRISPResso2 import CRISPResso2Align
 from CRISPResso2 import CRISPRessoCOREResources
 
@@ -1987,7 +1981,7 @@ def zip_results(results_folder):
 
 def is_C2Pro_installed():
     try:
-        spec = importlib.util.find_spec("crispressoPro")
+        spec = importlib.util.find_spec("CRISPRessoPro")
         if spec is None:
             return False
         else:
@@ -2032,8 +2026,7 @@ def check_custom_config(args):
     logger = logging.getLogger(getmodule(stack()[1][0]).__name__)
 
     #Check if crispresso.pro is installed
-    # if not is_C2Pro_installed():
-    if not pro_installed:
+    if not is_C2Pro_installed():
         return config
     if args.config_file:
         try:

diff --git a/CRISPResso2/CRISPRessoWGSCORE.py b/CRISPResso2/CRISPRessoWGSCORE.py
@@ -19,12 +19,6 @@
 from CRISPResso2 import CRISPRessoShared
 from CRISPResso2 import CRISPRessoMultiProcessing
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
-
 
 import logging
 
@@ -350,7 +344,7 @@ def print_stacktrace_if_debug():
 
         args = parser.parse_args()
 
-        if args.use_matplotlib or not pro_installed:
+        if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
             from CRISPResso2 import CRISPRessoPlot
         else:
             from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/scripts/plotAmbiguous.py b/scripts/plotAmbiguous.py
@@ -9,11 +9,7 @@
 import numpy as np
 import pandas as pd
 import zipfile
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
+
 from CRISPResso2 import CRISPRessoShared
 
 def main():
@@ -31,7 +27,7 @@ def main():
 
     args = parser.parse_args()
 
-    if args.use_matplotlib or not pro_installed:
+    if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
         from CRISPResso2 import CRISPRessoPlot
     else:
         from CRISPRessoPro import plot as CRISPRessoPlot

diff --git a/scripts/plotCustomAllelePlot.py b/scripts/plotCustomAllelePlot.py
@@ -9,11 +9,6 @@
 import numpy as np
 import pandas as pd
 import zipfile
-try:
-    from CRISPRessoPro import __version__
-    pro_installed = True
-except:
-    pro_installed = False
 from CRISPResso2 import CRISPRessoShared
 import seaborn as sns
 import matplotlib
@@ -39,7 +34,7 @@ def main():
                         help='Use matplotlib for plotting instead of plotly/d3 when CRISPRessoPro is installed')
 
     args = parser.parse_args()
-    if args.use_matplotlib or not pro_installed:
+    if args.use_matplotlib or not CRISPRessoShared.is_C2Pro_installed():
         from CRISPResso2 import CRISPRessoPlot
     else:
         from CRISPRessoPro import plot as CRISPRessoPlot