Merge branch 'master' into sam/pyproject-setup

.github/workflows/pytest.yml

@@ -2,7 +2,7 @@ name: Run Pytest
 
 on:
   push:
-  
+
   pull_request:
     types: [opened, reopened]
 
@@ -20,9 +20,8 @@ jobs:
     - uses: actions/checkout@v3
 
     - name: Set up Conda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-          mamba-version: "*"
           channels: conda-forge,bioconda,defaults
           auto-activate-base: false
           activate-environment: test_env
@@ -32,15 +31,15 @@ jobs:
       run: |
         sudo apt-get update
         sudo apt-get install -y gcc g++ bowtie2 samtools libsys-hostname-long-perl
-        
+
     - name: Install Pytest
       run: |
         pip install pytest pytest-cov
-    
+
     - name: Install CRISPResso
       run: |
         pip install -e .
 
     - name: Run Pytest
-      run: | 
+      run: |
         pytest tests --cov CRISPResso2

CRISPResso2/CRISPRessoAggregateCORE.py

@@ -71,6 +71,7 @@ def main():
 
         parser.add_argument('--debug', help='Show debug messages', action='store_true')
         parser.add_argument('-v', '--verbosity', type=int, help='Verbosity level of output to the console (1-4), 4 is the most verbose', default=3)
+        parser.add_argument('--halt_on_plot_fail', action="store_true", help="Halt execution if a plot fails to generate")
 
         # CRISPRessoPro params
         parser.add_argument('--use_matplotlib', action='store_true',
@@ -131,6 +132,7 @@ def main():
             num_processes=n_processes,
             process_pool=process_pool,
             process_futures=process_futures,
+            halt_on_plot_fail=args.halt_on_plot_fail,
         )
 
         #glob returns paths including the original prefix

CRISPResso2/CRISPRessoBatchCORE.py

@@ -400,6 +400,7 @@ def main():
             num_processes=n_processes_for_batch,
             process_futures=process_futures,
             process_pool=process_pool,
+            halt_on_plot_fail=args.halt_on_plot_fail,
         )
 
         window_nuc_pct_quilt_plot_names = []

CRISPResso2/CRISPRessoCORE.py

@@ -1434,6 +1434,11 @@ def print_stacktrace_if_debug():
 
         logger.addHandler(CRISPRessoShared.StatusHandler(os.path.join(OUTPUT_DIRECTORY, 'CRISPResso_status.json')))
 
+        if C2PRO_INSTALLED:
+            debug(f'CRISPRessoPro v{CRISPRessoProVersion} installed', {'percent_complete': 0.5})
+        else:
+            debug(f'CRISPRessoPro not installed', {'percent_complete': 0.5})
+
         aln_matrix_loc = os.path.join(_ROOT, "EDNAFULL")
         CRISPRessoShared.check_file(aln_matrix_loc)
         aln_matrix = CRISPResso2Align.read_matrix(aln_matrix_loc)
@@ -1978,10 +1983,6 @@ 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 C2PRO_INSTALLED:
-            info(f'CRISPRessoPro v{CRISPRessoProVersion} installed', {'percent_complete': 3})
-        else:
-            info(f'CRISPRessoPro not installed', {'percent_complete': 3})
 
         found_guide_seq = [False]*len(guides)
         found_coding_seq = [False]*len(coding_seqs)
@@ -2021,14 +2022,14 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited
                     #for all amps in forward and reverse complement amps:
                     for amp_seq in [this_seq, CRISPRessoShared.reverse_complement(this_seq)]:
                         ref_incentive = np.zeros(len(amp_seq)+1, dtype=int)
-                        s1, s2, score=CRISPResso2Align.global_align(guide, amp_seq, matrix=aln_matrix, gap_incentive=ref_incentive, gap_open=args.needleman_wunsch_gap_open, gap_extend=args.needleman_wunsch_gap_extend,)
+                        s1, s2, score=CRISPResso2Align.global_align(guide, amp_seq, matrix=aln_matrix, gap_incentive=ref_incentive, gap_open=args.flexiguide_gap_open_penalty, gap_extend=args.flexiguide_gap_extend_penalty)
                         potential_guide = s1.strip("-")
                         if abs(len(potential_guide) - len(guide)) < 2: #if length of putative guide is off by less than 2, keep it (allows 1 gap)
                             loc = s1.find(potential_guide)
                             potential_ref = amp_seq[loc:loc+len(potential_guide)]
                             #realign to test for number of mismatches
                             ref_incentive = np.zeros(len(potential_ref)+1, dtype=int)
-                            sub_s1, sub_s2, sub_score=CRISPResso2Align.global_align(guide, potential_ref, matrix=aln_matrix, gap_incentive=ref_incentive, gap_open=args.needleman_wunsch_gap_open, gap_extend=args.needleman_wunsch_gap_extend,)
+                            sub_s1, sub_s2, sub_score=CRISPResso2Align.global_align(guide, potential_ref, matrix=aln_matrix, gap_incentive=ref_incentive, gap_open=args.flexiguide_gap_open_penalty, gap_extend=args.flexiguide_gap_extend_penalty)
                             mismatches = []
                             for i in range(len(sub_s1)):
                                 if sub_s1[i] != sub_s2[i]:
@@ -3749,6 +3750,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
             num_processes=n_processes,
             process_pool=process_pool,
             process_futures=process_futures,
+            halt_on_plot_fail=args.halt_on_plot_fail,
         )
         ###############################################################################################################################################
         ### FIGURE 1: Alignment
@@ -5177,6 +5179,10 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
         print_stacktrace_if_debug()
         error('Filtering error, please check your input.\n\nERROR: %s' % e)
         sys.exit(13)
+    except CRISPRessoShared.PlotException as e:
+        print_stacktrace_if_debug()
+        error(e)
+        sys.exit(14)
     except Exception as e:
         print_stacktrace_if_debug()
         error('Unexpected error, please check your input.\n\nERROR: %s' % e)