fix

app.py

@@ -9,6 +9,8 @@ import plotly.graph_objs as go
 from pygenomeviz import Genbank, GenomeViz
 import numpy as np
 from pathlib import Path
+import zipfile
+import io
 
 
 # title and documentation
@@ -21,6 +23,10 @@ selected_model = st.selectbox('Select CRISPR model:', CRISPR_MODELS, key='select
 cas9on_path = 'cas9_model/on-cla.h5'
 cas12_path = 'cas12_model/Seq_deepCpf1_weights.h5'
 
+# Links for user guidance on using the downloaded files
+st.markdown("GenBank files can be visualized using [PyGenomeViz](https://pygenomeviz.streamlit.app/). "
+            "BED files can be used with the [UCSC Genome Browser](https://genome.ucsc.edu/cgi-bin/hgCustom).")
+
 @st.cache_data
 def convert_df(df):
             # IMPORTANT: Cache the conversion to prevent computation on every rerun
@@ -214,26 +220,24 @@ if selected_model == 'Cas9':
                     cas9on.create_bed_file_from_df(df, bed_file_path)
                     cas9on.create_csv_from_df(df, csv_file_path)
 
-                    # Layout for download buttons
-                    col1, col2, col3 = st.columns(3)
-                    with col1:
-                        with open(genbank_file_path, "rb") as file:
-                            st.download_button(label="Download GenBank File", data=file, file_name=genbank_file_path,
-                                               mime="text/x-genbank")
-                    with col2:
-                        with open(bed_file_path, "rb") as file:
-                            st.download_button(label="Download BED File", data=file, file_name=bed_file_path,
-                                               mime="text/plain")
-                    with col3:
-                        with open(csv_file_path, "rb") as file:
-                            st.download_button(label="Download CSV File", data=file, file_name=csv_file_path,
-                                               mime="text/csv")
-
-                    # Links for user guidance on using the downloaded files
-                    st.markdown(
-                        "GenBank files can be visualized using [PyGenomeViz](https://pygenomeviz.streamlit.app/). "
-                        "BED files can be used with the [UCSC Genome Browser](https://genome.ucsc.edu/cgi-bin/hgCustom).")
+                    # Prepare an in-memory buffer for the ZIP file
+                    zip_buffer = io.BytesIO()
+                    with zipfile.ZipFile(zip_buffer, 'w', zipfile.ZIP_DEFLATED) as zip_file:
+                        # For each file, add it to the ZIP file
+                        zip_file.write(genbank_file_path, arcname=genbank_file_path.split('/')[-1])
+                        zip_file.write(bed_file_path, arcname=bed_file_path.split('/')[-1])
+                        zip_file.write(csv_file_path, arcname=csv_file_path.split('/')[-1])
+
+                    # Important: move the cursor to the beginning of the BytesIO buffer before reading it
+                    zip_buffer.seek(0)
 
+                    # Display the download button for the ZIP file
+                    st.download_button(
+                        label="Download genbank,.bed,csv files as ZIP",
+                        data=zip_buffer.getvalue(),
+                        file_name=f"{gene_symbol}_files.zip",
+                        mime="application/zip"
+                    )
 
     elif target_selection == 'off-target':
         ENTRY_METHODS = dict(
@@ -422,40 +426,39 @@ elif selected_model == 'Cas12':
             st.plotly_chart(fig)
 
             # Ensure gene_sequence is not empty before generating files
-            if gene_sequence:
+            if 'gene_sequence' in st.session_state and st.session_state['gene_sequence']:
+                gene_symbol = st.session_state['current_gene_symbol']
+                gene_sequence = st.session_state['gene_sequence']
+
                 # Define file paths
                 genbank_file_path = f"{gene_symbol}_crispr_targets.gb"
                 bed_file_path = f"{gene_symbol}_crispr_targets.bed"
                 csv_file_path = f"{gene_symbol}_crispr_predictions.csv"
 
                 # Generate files
-                cas9on.generate_genbank_file_from_df(df, gene_sequence, gene_symbol, genbank_file_path)
-                cas9on.create_bed_file_from_df(df, bed_file_path)
-                cas9on.create_csv_from_df(df, csv_file_path)
-
-                # Layout for download buttons
-                col1, col2, col3 = st.columns(3)
-                with col1:
-                    with open(genbank_file_path, "rb") as file:
-                        st.download_button(label="Download GenBank File", data=file, file_name=genbank_file_path,
-                                           mime="text/x-genbank")
-                with col2:
-                    with open(bed_file_path, "rb") as file:
-                        st.download_button(label="Download BED File", data=file, file_name=bed_file_path,
-                                           mime="text/plain")
-                with col3:
-                    with open(csv_file_path, "rb") as file:
-                        st.download_button(label="Download CSV File", data=file, file_name=csv_file_path,
-                                           mime="text/csv")
-
-                # Links for user guidance on using the downloaded files
-                st.markdown(
-                    "GenBank files can be visualized using [PyGenomeViz](https://pygenomeviz.streamlit.app/). "
-                    "BED files can be used with the [UCSC Genome Browser](https://genome.ucsc.edu/cgi-bin/hgCustom)."
+                cas12.generate_genbank_file_from_data(df, gene_sequence, gene_symbol, genbank_file_path)
+                cas12.generate_bed_file_from_data(df, bed_file_path)
+                cas12.create_csv_from_df(df, csv_file_path)
+
+                # Prepare an in-memory buffer for the ZIP file
+                zip_buffer = io.BytesIO()
+                with zipfile.ZipFile(zip_buffer, 'w', zipfile.ZIP_DEFLATED) as zip_file:
+                    # For each file, add it to the ZIP file
+                    zip_file.write(genbank_file_path, arcname=genbank_file_path.split('/')[-1])
+                    zip_file.write(bed_file_path, arcname=bed_file_path.split('/')[-1])
+                    zip_file.write(csv_file_path, arcname=csv_file_path.split('/')[-1])
+
+                # Important: move the cursor to the beginning of the BytesIO buffer before reading it
+                zip_buffer.seek(0)
+
+                # Display the download button for the ZIP file
+                st.download_button(
+                    label="Download genbank,.bed,csv files as ZIP",
+                    data=zip_buffer.getvalue(),
+                    file_name=f"{gene_symbol}_files.zip",
+                    mime="application/zip"
                 )
 
-
-
 elif selected_model == 'Cas13d':
         ENTRY_METHODS = dict(
         manual='Manual entry of single transcript',