Simkin modular merge

PMO_Builder.py

@@ -1,7 +1,6 @@
 import streamlit as st
 from src.format_page import render_header
 
-
 def main():
     render_header()
     # Introduction Section

conf/schema.json

@@ -8,13 +8,16 @@
         "alternatives": {
             "target_id": [
                 "locus",
-                "amplicon"
+                "amplicon",
+                "mip_id"
             ],
             "forward_primers": [
-                "fwd_primers"
+                "fwd_primers",
+                "extension_arm"
             ],
             "reverse_primers": [
-                "rev_primers"
+                "rev_primers",
+                "ligation_arm"
             ]
         }
     },
@@ -130,7 +133,8 @@
                 "locus",
                 "marker_id",
                 "amplicon",
-                "locus_id"
+                "locus_id",
+                "p_targetName"
             ],
             "asv": [
                 "amplicon_sequence_variant",
@@ -144,7 +148,9 @@
             "reads": [
                 "read_count",
                 "sequence_reads",
-                "read_depth"
+                "read_depth",
+                "c_barcodeCnt",
+                "c_readCnt"
             ]
         }
     },

pages/1_Panel_Information.py

@@ -7,7 +7,6 @@
 from src.format_page import render_header
 from src.utils import load_schema
 
-
 class PanelManager:
     def __init__(self, save_dir):
         self.save_dir = save_dir

pages/8_Create_Final_PMO.py

@@ -3,94 +3,116 @@
 import os
 from src.format_page import render_header
 
-current_directory = os.getcwd()  # Get the current working directory
-SAVE_DIR = os.path.join(current_directory, "PMO")
-os.makedirs(SAVE_DIR, exist_ok=True)
+def check_panel_info():
+    # PANEL INFO
+    if "panel_info" in st.session_state:
+        panel_info = st.session_state["panel_info"]
+        panel_id = ', '.join(panel_info["panel_info"].keys())
+        st.write("**Current Panel Information:**", panel_id)
+    else:
+        st.error(
+            "No panel information found. Please go to the Panel Information tab before proceeding.")
+    return panel_info, panel_id
 
-render_header()
-st.subheader("Create Final PMO", divider="gray")
+def check_specimen_info():
+    # SPECIMEN INFO
+    if "specimen_info" in st.session_state:
+        spec_samples = ', '.join(
+            list(st.session_state["specimen_info"].keys())[:10])
+        st.write("**Current Specimen Information for samples (showing first 10):** ",
+                 spec_samples, '...')
+    else:
+        st.error(
+            "No specimen information found. Please go to the Specimen Information tab before proceeding.")
 
-st.subheader("Components")
-# PANEL INFO
-if "panel_info" in st.session_state:
-    panel_info = st.session_state["panel_info"]
-    panel_id = ', '.join(panel_info["panel_info"].keys())
-    st.write("**Current Panel Information:**", panel_id)
-else:
-    st.error(
-        "No panel information found. Please go to the Panel Information tab before proceeding.")
+def check_experiment_info():
+    # EXPERIMENT INFO
+    if "experiment_info" in st.session_state:
+        experiment_samples = ', '.join(
+            list(st.session_state["experiment_info"].keys())[:10])
+        st.write("**Current Experiment Information for samples (showing first 10):** ",
+                 experiment_samples, '...')
+    else:
+        st.error(
+            "No experiment information found. Please go to the Experiment Information tab before proceeding.")
 
-# SPECIMEN INFO
-if "specimen_info" in st.session_state:
-    spec_samples = ', '.join(
-        list(st.session_state["specimen_info"].keys())[:10])
-    st.write("**Current Specimen Information for samples (showing first 10):** ",
-             spec_samples, '...')
-else:
-    st.error(
-        "No specimen information found. Please go to the Specimen Information tab before proceeding.")
+def check_microhaplotype_info():
+	# MICROHAPLOTYPE INFO
+	if "mhap_data" in st.session_state:
+	    bioinfo_id = ', '.join(st.session_state["mhap_data"]["microhaplotypes_detected"].keys()
+	                           )
+	    st.write(
+	        "**Current Microhaplotype Information from bioinformatics run:**", bioinfo_id)
+	else:
+	    st.error(
+	        "No microhaplotype information found. Please go to the Microhaplotype Information tab before proceeding.")
+	return bioinfo_id
 
-# EXPERIMENT INFO
-if "experiment_info" in st.session_state:
-    experiment_samples = ', '.join(
-        list(st.session_state["experiment_info"].keys())[:10])
-    st.write("**Current Experiment Information for samples (showing first 10):** ",
-             experiment_samples, '...')
-else:
-    st.error(
-        "No experiment information found. Please go to the Experiment Information tab before proceeding.")
+def check_demultiplexed_info():
+	# DEMULTIPLEXED INFO
+	if "demultiplexed_data" in st.session_state:
+	    # demultiplexed_data = st.session_state["demultiplexed_data"]
+	    demultiplexed_bioinfo_id = st.session_state["demultiplexed_data"].keys()
+	    st.write("**Current Demultiplexed Information from bioinformatics run:**",
+	             ', '.join(demultiplexed_bioinfo_id))
+	else:
+	    st.error(
+	        "No demultiplexed information found. Please go to the Demultiplexed Samples tab before proceeding.")
 
-# MICROHAPLOTYPE INFO
-if "mhap_data" in st.session_state:
-    bioinfo_id = ', '.join(st.session_state["mhap_data"]["microhaplotypes_detected"].keys()
-                           )
-    st.write(
-        "**Current Microhaplotype Information from bioinformatics run:**", bioinfo_id)
-else:
-    st.error(
-        "No microhaplotype information found. Please go to the Microhaplotype Information tab before proceeding.")
+def check_sequencing_info():
+	# SEQUENCING INFO
+	if "seq_info" in st.session_state:
+	    seq_info_id = st.session_state["seq_info"].keys(
+	    )
+	    st.write("**Current Sequencing Information had ID:**",
+	             ', '.join(seq_info_id))
+	else:
+	    st.error(
+	        "No sequencing information found. Please go to the Sequencing Information tab before proceeding.")
 
-# DEMULTIPLEXED INFO
-if "demultiplexed_data" in st.session_state:
-    # demultiplexed_data = st.session_state["demultiplexed_data"]
-    demultiplexed_bioinfo_id = st.session_state["demultiplexed_data"].keys()
-    st.write("**Current Demultiplexed Information from bioinformatics run:**",
-             ', '.join(demultiplexed_bioinfo_id))
-else:
-    st.error(
-        "No demultiplexed information found. Please go to the Demultiplexed Samples tab before proceeding.")
+def check_bioinformatics_info():
+	# BIOINFORMATICS INFO
+	if "bioinfo_infos" in st.session_state:
+	    bioinfo_info_id = st.session_state["bioinfo_infos"]["tar_amp_bioinformatics_info_id"]
+	    st.write("**Current Bioinformatics Information had ID:**", bioinfo_info_id)
+	else:
+	    st.error(
+	        "No bioinformatics information found. Please go to the Bioinformatics Information tab before proceeding.")
 
-# SEQUENCING INFO
-if "seq_info" in st.session_state:
-    seq_info_id = st.session_state["seq_info"].keys(
-    )
-    st.write("**Current Sequencing Information had ID:**",
-             ', '.join(seq_info_id))
-else:
-    st.error(
-        "No sequencing information found. Please go to the Sequencing Information tab before proceeding.")
+def merge_data(panel_info, panel_id, bioinfo_id):
+	# MERGE DATA
+	st.subheader("Merge Components to Final PMO")
+	if st.button("Merge Data"):
+	    formatted_pmo = {
+	        "experiment_infos": st.session_state["experiment_info"],
+	        "sequencing_infos": st.session_state["seq_info"],
+	        "specimen_infos": st.session_state["specimen_info"],
+	        "taramp_bioinformatics_infos": st.session_state["bioinfo_infos"],
+	        **st.session_state["mhap_data"],
+	        **panel_info,
+	        **st.session_state["demultiplexed_data"],
+	    }
+	    output_path = os.path.join(SAVE_DIR, f"{panel_id}_{bioinfo_id}.json")
+	    with open(output_path, "w") as f:
+	        json.dump(formatted_pmo, f, indent=4)
+	    st.success(f"Your PMO has been saved! It can be found here: {output_path}")
 
-# BIOINFORMATICS INFO
-if "bioinfo_infos" in st.session_state:
-    bioinfo_info_id = st.session_state["bioinfo_infos"]["tar_amp_bioinformatics_info_id"]
-    st.write("**Current Bioinformatics Information had ID:**", bioinfo_info_id)
-else:
-    st.error(
-        "No bioinformatics information found. Please go to the Bioinformatics Information tab before proceeding.")
+def run_components():
+    panel_info, panel_id=check_panel_info()
+    check_specimen_info()
+    check_experiment_info()
+    bioinfo_id=check_microhaplotype_info()
+    check_demultiplexed_info()
+    check_sequencing_info()
+    check_bioinformatics_info()
+    merge_data(panel_info, panel_id, bioinfo_id)
 
-# MERGE DATA
-st.subheader("Merge Components to Final PMO")
-if st.button("Merge Data"):
-    formatted_pmo = {
-        "experiment_infos": st.session_state["experiment_info"],
-        "sequencing_infos": st.session_state["seq_info"],
-        "specimen_infos": st.session_state["specimen_info"],
-        "taramp_bioinformatics_infos": st.session_state["bioinfo_infos"],
-        **st.session_state["mhap_data"],
-        **panel_info,
-        **st.session_state["demultiplexed_data"],
-    }
-    output_path = os.path.join(SAVE_DIR, f"{panel_id}_{bioinfo_id}.json")
-    with open(output_path, "w") as f:
-        json.dump(formatted_pmo, f, indent=4)
-    st.success(f"Your PMO has been saved! It can be found here: {output_path}")
+# Initialize and run the app
+if __name__ == "__main__":
+    current_directory = os.getcwd()  # Get the current working directory
+    SAVE_DIR = os.path.join(current_directory, "finished_PMO_files")
+    os.makedirs(SAVE_DIR, exist_ok=True)
+    render_header()
+    st.subheader("Create Final PMO", divider="gray")
+    st.subheader("Components")
+    run_components()