wip: fixing comments

hiyama341 · Sep 26, 2024 · c0750bc · c0750bc
1 parent 09058fa
commit c0750bc
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Showing 4 changed files with 8 additions and 14 deletions.
diff --git a/web_app/callbacks/workflow_3.py b/web_app/callbacks/workflow_3.py
@@ -224,10 +224,11 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                 logger.info("Golden Gate Cloning setup completed.")
 
 
-                # Primer generation, analysis, and gel electrophoresis simulation
+                # Primer generation, analysis
                 primer_df = golden_gate.generate_primer_dataframe()
                 logger.info(f"Primer dataframe generated: {primer_df.shape[0]} rows")
-
+
+                # TODO maybe remove this redundancy.
                 analyze_primers_and_hairpins(primer_df)
                 logger.info("Primers analyzed for hairpins.")
 

diff --git a/web_app/callbacks/workflow_4.py b/web_app/callbacks/workflow_4.py
@@ -193,7 +193,7 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                 ]
 
                 output_files = [
-                    {"name": "cBEST_w_sgRNAs.gb", "content": sgRNA_vectors},
+                    {"name": "CRISPRi_w_sgRNAs.gb", "content": sgRNA_vectors},
                     {"name": "full_idt.csv", "content": idt_primers},
                     {"name": "sgrna_df.csv", "content": sgrna_df},
                     {"name": "filtered_df.csv", "content": filtered_df}

diff --git a/web_app/callbacks/workflow_5.py b/web_app/callbacks/workflow_5.py
@@ -161,9 +161,6 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                 logging.info("Filtering sgRNAs ")
                 filtered_df = sgrna_df.groupby('locus_tag').head(number_of_sgRNAs_per_group)
 
-                # Filter the DataFrame to retain only up to 5 sgRNA sequences per locus_tag
-                filtered_df = sgrna_df.groupby('locus_tag').head(number_of_sgRNAs_per_group)
-
                 # MAke oligoes
                 list_of_ssDNAs = make_ssDNA_oligos(filtered_df, upstream_ovh = up_homology,
                                     downstream_ovh=dw_homology)
@@ -216,8 +213,6 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                     logging.info(f"repair_templates_data: {repair_templates_data}")
                     logging.info(f"overlap_for_gibson_length: {overlap_for_gibson_length}")
 
-
-                    # TODO ASSEMBLY DATA DOES NOT YIELD ANY DATA - IT OUTPUTS AND EMPTY list - fix soon
                     # Assembly 
                     assembly_data = assemble_multiple_plasmids_with_repair_templates_for_deletion(genes_to_KO_list, 
                                                                                                   processed_records, 
@@ -302,7 +297,7 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
 
                 if in_frame_deletion: 
                     output_files = [
-                        {"name": "cBEST_w_sgRNAs.gb", "content": assembled_contigs}, # LIST OF Dseqrecords
+                        {"name": "Cas9_w_sgRNAs.gb", "content": assembled_contigs}, # LIST OF Dseqrecords
                         {"name": "primer_df.csv", "content": unique_df},
                         {"name": "full_idt.csv", "content": full_idt},
                         {"name": "sgrna_df.csv", "content": sgrna_df},
@@ -314,7 +309,7 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                     ]
                 else: 
                     output_files = [
-                        {"name": "cBEST_w_sgRNAs.gb", "content": sgRNA_vectors}, # LIST OF Dseqrecords
+                        {"name": "Cas9_sgRNAs.gb", "content": sgRNA_vectors}, # LIST OF Dseqrecords
                         {"name": "full_idt.csv", "content": full_idt},
                         {"name": "sgrna_df.csv", "content": sgrna_df},
                         {"name": "filtered_df.csv", "content": filtered_df},

diff --git a/web_app/callbacks/workflow_6.py b/web_app/callbacks/workflow_6.py
@@ -122,7 +122,6 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
             # Initialize variables to avoid UnboundLocalError
             logging.info("Initializing variables.")
             primer_df = pd.DataFrame()
-            idt_df_with_repair = pd.DataFrame()
             unique_df = pd.DataFrame()
 
             # Create a temporary directory
@@ -211,7 +210,6 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                                                                         primer_tm_kwargs={'conc':primer_concentration, 'prodcode':chosen_polymerase} , 
                                                                         repair_length=repair_templates_length)
                     # Convert the string to an enzyme object
-                    #enzyme_for_repair_template_integration = getattr(__import__('Bio.Restriction'), enzyme_for_repair_template_integration)
                     enzyme = getattr(Restriction, str(enzyme_for_repair_template_integration))
 
                     logging.info("Digesting plasmids with enzyme_for_repair_template_integration.")
@@ -307,7 +305,7 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                 if in_frame_deletion: 
                     logging.info("Preparing output files for project directory with in-frame deletion.")
                     output_files = [
-                        {"name": "BEST_w_sgRNAs.gb", "content": assembled_contigs}, # LIST OF Dseqrecords
+                        {"name": "Cas3_w_sgRNAs.gb", "content": assembled_contigs}, # LIST OF Dseqrecords
                         {"name": "primer_df.csv", "content": primer_df},
                         {"name": "full_idt.csv", "content": full_idt},
                         {"name": "sgrna_df.csv", "content": sgrna_df},
@@ -319,7 +317,7 @@ def run_workflow(n_clicks, genome_content, vector_content, genome_filename, vect
                 else: 
                     logging.info("Preparing output files for project directory without in-frame deletion.")
                     output_files = [
-                        {"name": "cBEST_w_sgRNAs.gb", "content": assembled_cas3_plasmids}, # LIST OF Dseqrecords
+                        {"name": "Cas3_sgRNAs.gb", "content": assembled_cas3_plasmids}, # LIST OF Dseqrecords
                         {"name": "full_idt.csv", "content": full_idt},
                         {"name": "sgrna_df.csv", "content": sgrna_df},
                         {"name": "filtered_df.csv", "content": filtered_df},