fixed bugs

app.py

@@ -136,35 +136,46 @@ if selected_model == 'Cas9':
                 # Now create a Plotly plot with the sorted_predictions
                 fig = go.Figure()
 
-                # Set y values based on strand information
-                strand_y_values = {'1': 1, '-1': -1}
+                # Variables to help spread gRNAs on the y-axis based on their strand
+                y_positive_strand = 10
+                y_negative_strand = -10
+                strand_offset = 1  # This will space out each subsequent guide on the same strand
 
                 # Iterate over the sorted predictions to create the plot
                 for i, prediction in enumerate(sorted_predictions, start=1):
                     # Extract data for plotting
-                    chrom, start, end, strand, target, gRNA, pred_score = prediction  # Adjusted to include the target sequence
-                    # Assign y value based on strand
-                    y_value = strand_y_values[str(strand)]  # Convert strand to string for dict lookup
+                    chrom, start, end, strand, target, gRNA, pred_score = prediction
+                    y_value = y_positive_strand if strand == 1 else y_negative_strand
                     fig.add_trace(go.Scatter(
                         x=[start, end],
-                        y=[y_value] * len(start),  # Assign all points the same y value based on strand
+                        y=[y_value, y_value],  # Assign all points the same y value based on strand
                         mode='lines+markers+text',
                         name=f"gRNA: {gRNA}",
-                        text=f"Rank: {i}",  # Place text at the first point
+                        text=[f"Rank: {i}", ""],  # Text at the start position only
                         hoverinfo='text',
-                        hovertext=f"Rank: {i}<br>Chromosome: {chrom}<br>Target Sequence: {target}<br>gRNA: {gRNA}<br>Start: {start}<br>End: {end}<br>Strand: {'+' if strand == '1' else '-'}<br>Prediction Score: {pred_score:.4f}",
+                        hovertext=[
+                            f"Rank: {i}<br>Target: {target}<br>gRNA: {gRNA}<br>Cutsite: {start}<br>On Target Score: {pred_score:.4f}",
+                            ""
+                        ],
                     ))
+                    # Update the y-value for the next guide on the same strand
+                    if strand == 1:
+                        y_positive_strand += strand_offset
+                    else:
+                        y_negative_strand -= strand_offset
 
                 # Update the layout of the plot
                 fig.update_layout(
-                    title='CRISPR Targets by Strand',
+                    title='Top 10 gRNA Sequences by Prediction Score',
                     xaxis_title='Genomic Position',
+                    yaxis_title='Strand',
                     yaxis=dict(
-                        title='Strand',
-                        tickmode='array',
-                        tickvals=[1, -1],
-                        ticktext=['+ Strand', '- Strand']
-                    )
+                        showgrid=True,  # Show horizontal gridlines for clarity
+                        zeroline=True,  # Show a line at y=0
+                        zerolinecolor='Black',
+                        zerolinewidth=2,
+                    ),
+                    showlegend=False  # Hide the legend if it's not necessary
                 )
 
                 # Display the plot
@@ -351,35 +362,46 @@ elif selected_model == 'Cas12':
             # Now create a Plotly plot with the sorted_predictions
             fig = go.Figure()
 
-            # Set y values based on strand information
-            strand_y_values = {'1': 1, '-1': -1}
+            # Variables to help spread gRNAs on the y-axis based on their strand
+            y_positive_strand = 10
+            y_negative_strand = -10
+            strand_offset = 1  # This will space out each subsequent guide on the same strand
 
             # Iterate over the sorted predictions to create the plot
             for i, prediction in enumerate(sorted_predictions, start=1):
                 # Extract data for plotting
-                chrom, start, end, strand, target, gRNA, pred_score = prediction  # Adjusted to include the target sequence
-                # Assign y value based on strand
-                y_value = strand_y_values[str(strand)]  # Convert strand to string for dict lookup
+                chrom, start, end, strand, target, gRNA, pred_score = prediction
+                y_value = y_positive_strand if strand == 1 else y_negative_strand
                 fig.add_trace(go.Scatter(
                     x=[start, end],
-                    y=[y_value] * len(start),  # Assign all points the same y value based on strand
+                    y=[y_value, y_value],  # Assign all points the same y value based on strand
                     mode='lines+markers+text',
                     name=f"gRNA: {gRNA}",
-                    text=f"Rank: {i}",  # Place text at the first point
+                    text=[f"Rank: {i}", ""],  # Text at the start position only
                     hoverinfo='text',
-                    hovertext=f"Rank: {i}<br>Chromosome: {chrom}<br>Target Sequence: {target}<br>gRNA: {gRNA}<br>Start: {start}<br>End: {end}<br>Strand: {'+' if strand == '1' else '-'}<br>Prediction Score: {pred_score:.4f}",
+                    hovertext=[
+                        f"Rank: {i}<br>Target: {target}<br>gRNA: {gRNA}<br>Cutsite: {start}<br>On Target Score: {pred_score:.4f}",
+                        ""
+                    ],
                 ))
+                # Update the y-value for the next guide on the same strand
+                if strand == 1:
+                    y_positive_strand += strand_offset
+                else:
+                    y_negative_strand -= strand_offset
 
             # Update the layout of the plot
             fig.update_layout(
-                title='CRISPR Targets by Strand',
+                title='Top 10 gRNA Sequences by Prediction Score',
                 xaxis_title='Genomic Position',
+                yaxis_title='Strand',
                 yaxis=dict(
-                    title='Strand',
-                    tickmode='array',
-                    tickvals=[1, -1],
-                    ticktext=['+ Strand', '- Strand']
-                )
+                    showgrid=True,  # Show horizontal gridlines for clarity
+                    zeroline=True,  # Show a line at y=0
+                    zerolinecolor='Black',
+                    zerolinewidth=2,
+                ),
+                showlegend=False  # Hide the legend if it's not necessary
             )
 
             # Display the plot
@@ -417,8 +439,7 @@ elif selected_model == 'Cas12':
                         st.download_button(label="Download CSV File", data=file, file_name=csv_file_path,
                                            mime="text/csv")
 
-                # Clean up old files after download buttons are created
-                clean_up_old_files(gene_symbol)
+
 
 elif selected_model == 'Cas13d':
         ENTRY_METHODS = dict(