feat: analysis of low cfDNA input updated for comparison to QG

.gitignore

@@ -188,3 +188,4 @@ cython_debug/
 # PyPI configuration file
 .pypirc
 
+data/

notebooks/initial_eda_lb_20250919.py

@@ -1,6 +1,6 @@
 import marimo
 
-__generated_with = "0.14.16"
+__generated_with = "0.16.4"
 app = marimo.App(width="medium")
 
 
@@ -168,7 +168,7 @@ def _(mo):
 def _(os, pd, qc_hist_dir):
     # QG historical data
     qg_hist_stats = pd.read_csv(
-        os.path.join(qc_hist_dir, "historical_data_LB.csv"), index_col=0
+        os.path.join(qc_hist_dir, "historical_data_LB-QG.csv"), index_col=0
     )
     qg_hist_stats.columns = [i.replace("|", " / ") for i in qg_hist_stats.columns]
     qg_hist_stats = qg_hist_stats.drop(["batch"], axis=1)
@@ -866,6 +866,33 @@ def _(clinicals, meta, pd, stats):
     return (stats_meta,)
 
 
+@app.cell
+def _(pd):
+    meta_qg = pd.read_excel(
+        "/home/darren/Documents/4_data/3_internal/2_lb/QC/lb2_metadata.xlsx",
+        index_col="fastq_id",
+    )
+    meta_qg
+    return (meta_qg,)
+
+
+@app.cell
+def _(meta_qg, pd, qg_hist_stats):
+    # merge stats and metadata and remove seracares
+    stats_meta_qg = pd.concat([qg_hist_stats, meta_qg], axis=1)
+    stats_meta_qg = stats_meta_qg.loc[
+        [
+            i
+            for i in stats_meta_qg.index
+            if "twist" not in i.lower() and "sera" not in i.lower()
+        ],
+        :,
+    ]
+    stats_meta_qg = stats_meta_qg.reset_index()
+    stats_meta_qg.head()
+    return (stats_meta_qg,)
+
+
 @app.cell
 def _(mo, stats_meta):
     var1 = mo.ui.dropdown(options=stats_meta.columns, label="Variable 1")
@@ -975,6 +1002,108 @@ def _(stats_meta):
     return
 
 
+@app.cell
+def _(stats_meta_melt):
+    stats_meta_melt["Flow cell #"].unique()
+    return
+
+
+@app.cell
+def _(qg_hist_stats):
+    qg_hist_stats
+    return
+
+
+@app.cell
+def _(pd, stats_meta, stats_meta_qg):
+    stats_meta["lab"] = "Serenomica"
+    stats_meta_qg["lab"] = "Quantgene"
+    all_stats_meta = pd.concat([stats_meta, stats_meta_qg], axis=0)
+    all_stats_meta.shape
+    return (all_stats_meta,)
+
+
+@app.cell
+def _(all_stats_meta):
+    all_stats_meta["ng_group"] = [
+        "< 30ng" if i < 30 else "> 30ng"
+        for i in all_stats_meta["Input DNA used (ng)"]
+    ]
+    all_stats_meta[["lab", "ng_group"]].value_counts()
+    return
+
+
+@app.cell
+def _(all_stats_meta, pd):
+    all_stats_meta_melt = pd.melt(
+        all_stats_meta,
+        id_vars=["index", "sample_type", "ng_group", "Flow cell #", "lab"],
+    )
+    all_stats_meta_melt
+    return (all_stats_meta_melt,)
+
+
+@app.cell
+def _(all_stats_meta_melt, mo):
+    box_vars2 = mo.ui.dropdown(
+        options=all_stats_meta_melt["variable"].unique(), label="Variables to plot"
+    )
+    mo.hstack([box_vars2])
+    return (box_vars2,)
+
+
+@app.cell
+def _(all_stats_meta_melt, box_vars2, px):
+    fig7 = px.box(
+        data_frame=all_stats_meta_melt.loc[
+            (all_stats_meta_melt["variable"] == box_vars2.value)
+        ],
+        color="ng_group",
+        y="value",
+        x="lab",
+        template="simple_white",
+        points="all",
+        labels={
+            "ng_group": "cfDNA Input for Library",
+            "value": box_vars2.value,
+            "lab": "Laboratory",
+        },
+        color_discrete_sequence=px.colors.qualitative.Dark2,
+        category_orders={"ng_group": ["< 30ng", "> 30ng"]},
+        hover_data=["index"],
+        width=800,
+    )
+    fig7.update_traces(
+        marker=dict(size=10, line=dict(width=1, color="DarkSlateGrey")),
+        selector=dict(type="points"),
+    )
+    fig7.update_xaxes(tickfont_size=14)
+    fig7.update_yaxes(showgrid=True, tickfont_size=14)
+    fig7.update_legends(font_size=14)
+
+    for trace2 in fig7.select_traces():
+        trace2.marker.update(
+            size=7, line=dict(width=1, color="DarkSlateGrey"), opacity=0.8
+        )
+
+    fig7.show()
+    return
+
+
+@app.cell
+def _(all_stats_meta):
+    all_stats_meta[["lab", "ng_group"]].value_counts()
+    return
+
+
+@app.cell
+def _(stats_meta):
+    stats_meta.sort_values("Input DNA used (ng)")[
+        ["index", "Input DNA used (ng)", "Flow cell #"]
+    ]
+    return
+
+
 @app.cell
 def _():
     return

src/get_panel_coverage.py

@@ -10,7 +10,9 @@ logging.basicConfig(
 )
 
 
-def main(s3_paths: list[str], bed_path: str, ref_path: str, cli_bin: str) -> None:
+def main(
+    s3_paths: list[str], bed_path: str, ref_path: str, cli_bin: str, tars: bool
+) -> None:
     logging.info("Script started...")
     logging.info(f"Using reference: {ref_path}")
     logging.info(f"Using bed file: {bed_path}")
@@ -22,12 +24,21 @@ def main(s3_paths: list[str], bed_path: str, ref_path: str, cli_bin: str) -> Non
         file_num = f"{idx+1}/{len(s3_paths)}"
 
         logging.info(f"({file_num}) Downloading file: {name}")
-        down_cmd = (
+        if tars:
-            f"{cli_bin} s3 cp {file} . --profile=se"
+            down_unpack_cmd = (
-            if cli_bin == "aws"
+                f"{cli_bin} s3 cp {file} . --profile=se"
-            else f"{cli_bin} get {file} ."
+                if cli_bin == "aws"
-        )
+                else f"{cli_bin} get {file} . && tar -xf {name} --strip-components=4 --wildcards --no-anchored '*.cram' && rm {name}"
-        run(down_cmd, shell=True, capture_output=False)
+            )
+            run(down_unpack_cmd, shell=True, capture_output=False)
+            name = name.split(".")[0] + ".collapsed.cram"
+        else:
+            down_cmd = (
+                f"{cli_bin} s3 cp {file} . --profile=se"
+                if cli_bin == "aws"
+                else f"{cli_bin} get {file} ."
+            )
+            run(down_cmd, shell=True, capture_output=False)
 
         sort_name = f"{name.split('.')[0]}.sorted.cram"
         sort_cmd = f"samtools sort -@ 18 {name} --reference {ref_path} > {sort_name}"
@@ -47,40 +58,83 @@ def main(s3_paths: list[str], bed_path: str, ref_path: str, cli_bin: str) -> Non
 
 if __name__ == "__main__":
     s3_paths = [
-        # "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-25-0001-pa-21Mar2025_S33.collapsed.cram",
+        # "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0087-pa-13Jun2023_S1.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-25-0002-pa-21Mar2025_S34.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0089-pa-13Jun2023_S2.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-25-0003-pa-21Mar2025_S35.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0090-pa-13Jun2023_S3.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-25-0004-pa-21Mar2025_S36.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0091-pa-13Jun2023_S4.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-25-0005-pa-21Mar2025_S37.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0092-pa-13Jun2023_S5.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-25-0006-pa-21Mar2025_S38.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0096-pa-13Jun2023_S6.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0d125pc-1-28Mar2025_S41.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0098-pa-29Jun2023_S1.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0d125pc-2-28Mar2025_S42.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0099-pa-29Jun2023_S2.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0d25pc-1-28Mar2025_S43.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0100-pa-29Jun2023_S3.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0d25pc-2-28Mar2025_S44.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0103-pa-29Jun2023_S4.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0d5pc-1-28Mar2025_S45.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0105-pa-29Jun2023_S5.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0d5pc-2-28Mar2025_S46.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0107-pa-29Jun2023_S6.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0pc-1-28Mar2025_S39.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0112-pa-19Jul2023_S1.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-0pc-2-28Mar2025_S40.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0113-pa-19Jul2023_S2.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-1pc-1-28Mar2025_S48.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0119-pa-19Jul2023_S4.bams.tar",
-        "s3://serenomica-pipeline-archive/se1-prd-2.1.1/LB-SeraPlasma-1pc-2-28Mar2025_S47.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0122-pa-19Jul2023_S5.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0007-pa-1-23May2025_S20.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0123-pa-19Jul2023_S6.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0007-pa-2-23May2025_S21.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0124-pa-19Jul2023_S7.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0008-pa-1-23May2025_S22.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0125-pa-19Jul2023_S8.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0008-pa-2-23May2025_S23.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0126-pa-19Jul2023_S9.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0009-pa-1-23May2025_S24.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0128-pa-19Jul2023_S10.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0009-pa-2-23May2025_S25.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0129-pa-19Jul2023_S3.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0010-pa-1-23May2025_S26.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0130-pa-09Aug2023_S1.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0010-pa-2-23May2025_S27.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0132-pa-09Aug2023_S2.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0011-pa-1-23May2025_S32.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0133-pa-09Aug2023_S3.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0012-pa-1-23May2025_S28.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0134-pa-09Aug2023_S4.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0012-pa-2-23May2025_S29.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0135-pa-09Aug2023_S5.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0032-pa-1-23May2025_S30.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0136-pa-09Aug2023_S6.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-25-0032-pa-2-23May2025_S31.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0137-pa-09Aug2023_S7.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-SeraCare-0d25pc-1-21Mar2025_S17.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0138-pa-30Aug2023_S1.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-SeraCare-0d25pc-2-21Mar2025_S18.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0140-pa-30Aug2023_S2.bams.tar",
-        "s3://serenomica-pipeline-archive/se2-lb-1/LB-SeraPlasma-0pc-3-28Mar2025_S19.collapsed.cram",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0141-pa-30Aug2023_S3.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0142-pa-30Aug2023_S4.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0144-pa-30Aug2023_S5.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0145-pa-30Aug2023_S6.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0146-pa-30Aug2023_S7.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0147-pa-30Aug2023_S8.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0153-pa-25Oct2023_S1.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0156-pa-25Oct2023_S2.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0159-pa-25Oct2023_S3.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0160-pa-25Oct2023_S4.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-23-0186-pa-14Feb2024_S1.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0001-pa-14Feb2024_S2.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0015-pa-14Feb2024_S3.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0019-pa-14Feb2024_S4.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0023-pa-14Feb2024_S5.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0024-pa-14Feb2024_S6.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0027-pa-14Feb2024_S7.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0037-pa-28Mar2024_S16.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0038-pa-28Mar2024_S17.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0044-pa-13May2024_S2.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0046-pa-13May2024_S3.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0047-pa-13May2024_S4.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0047-pa-23May2024_S1.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0048-pa-13May2024_S5.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0049-pa-13May2024_S6.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0049-pa-23May2024_S2.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0050-pa-13May2024_S7.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0050-pa-23May2024_S3.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0053-pa-13May2024_S8.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0053-pa-23May2024_S4.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0054-pa-13May2024_S9.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0055-pa-13May2024_S10.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0056-pa-13May2024_S11.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0057-pa-13May2024_S12.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0058-pa-13May2024_S13.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0059-pa-23May2024_S5.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0060-pa-23May2024_S6.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0063-pa-23May2024_S7.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0064-pa-23May2024_S8.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-24-0065-pa-23May2024_S9.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-GVA-HC-246-13Jun2023_S10.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-GVA-ME-339-13Jun2023_S9.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-GVA-PA-307-13Jun2023_S8.bams.tar",
+        "s3://serenomica-pipeline-archive/historical-qg-qc-samples/LB-GVA-PA-308-13Jun2023_S7.bams.tar",
     ]
     # "/home/darren/Documents/4_data/3_internal/1_panels/TWIST/twist_LB_probes_plus_30bp_merged.sorted.bed"
-    bed_path = "/home/darren/Documents/4_data/3_internal/1_panels/TWIST/twist_LB_probes_plus_30bp_merged.sorted.bed"
+    bed_path = "/home/darren/Documents/4_data/3_internal/1_panels/Aglient/LB_3413441_Covered_50ext.sorted.bed"
     ref_path = "/home/darren/Documents/4_data/1_genomes/human/hg38/Homo_sapiens_assembly38.fasta"
-    main(s3_paths, bed_path, ref_path, cli_bin="aws")
+    main(s3_paths, bed_path, ref_path, cli_bin="s3cmd", tars=True)