New script: Saphyr average concentration and CV calculation (#479) (m…

…inor)

### Added

- New script to calculate average concentration and CV value for Saphyr samples

cg_lims/EPPs/udf/calculate/base.py

@@ -14,6 +14,7 @@
 from cg_lims.EPPs.udf.calculate.calculate_resuspension_buffer_volumes import (
     calculate_resuspension_buffer_volume,
 )
+from cg_lims.EPPs.udf.calculate.calculate_saphyr_concentration import calculate_saphyr_concentration
 from cg_lims.EPPs.udf.calculate.calculate_water import volume_water
 from cg_lims.EPPs.udf.calculate.calculate_water_volume_rna import calculate_water_volume_rna
 from cg_lims.EPPs.udf.calculate.get_missing_reads import get_missing_reads
@@ -60,5 +61,6 @@ def calculate(ctx):
 calculate.add_command(novaseq_x_volumes)
 calculate.add_command(pool_normalization)
 calculate.add_command(novaseq_x_denaturation)
+calculate.add_command(calculate_saphyr_concentration)
 calculate.add_command(ont_aliquot_volume)
 calculate.add_command(ont_available_sequencing_reload)

cg_lims/EPPs/udf/calculate/calculate_saphyr_concentration.py

@@ -0,0 +1,92 @@
+import logging
+import sys
+from typing import List
+
+import click
+import numpy as np
+from cg_lims.exceptions import LimsError, MissingUDFsError
+from cg_lims.get.artifacts import get_artifacts
+from genologics.entities import Artifact
+
+LOG = logging.getLogger(__name__)
+
+
+def get_concentrations(artifact: Artifact) -> List[float]:
+    """Returns a list of all concentration replicates called
+    Concentration 1 (ng/ul), Concentration 2 (ng/ul) and Concentration 3 (ng/ul) of an artifact."""
+    udf_names = ["Concentration 1 (ng/ul)", "Concentration 2 (ng/ul)", "Concentration 3 (ng/ul)"]
+    concentrations = []
+    for name in udf_names:
+        concentrations.append(artifact.udf.get(name))
+    return concentrations
+
+
+def calculate_average_concentration(concentrations: List[float]) -> float:
+    """Returns the average concentration of the list concentrations"""
+    return float(np.mean(concentrations))
+
+
+def calculate_cv(concentrations: List[float]) -> float:
+    """Calculates the coefficient of variance of the concentrations with the average concentration
+    that was retrieved from calculate_average_concentration"""
+    average_concentration = np.mean(concentrations)
+    std_deviation = np.std(concentrations)
+    coefficient_variation = std_deviation / average_concentration
+    return coefficient_variation
+
+
+def set_average_and_cv(artifact: Artifact) -> None:
+    """Calls on the previous functions get_concentration, calculate_average_concentration and calculate_cv
+    and updates the UDFs Average concentration (ng/ul) and Coefficient of variation (CV) with the calculated values
+    """
+    concentrations = get_concentrations(artifact=artifact)
+    average_concentration = calculate_average_concentration(concentrations=concentrations)
+    coefficient_variation = calculate_cv(concentrations=concentrations)
+
+    artifact.udf["Average concentration (ng/ul)"] = average_concentration
+    artifact.udf["Coefficient of variation (CV)"] = coefficient_variation
+    artifact.put()
+
+
+def validate_udf_values(artifact: Artifact) -> bool:
+    """A function checking whether a concentration in the list of concentrations for each artifact has a negative/no/zero value.
+    Then the function returns the output as 'False' and logs all those sample IDs in the EPP log"""
+    udf_names = ["Concentration 1 (ng/ul)", "Concentration 2 (ng/ul)", "Concentration 3 (ng/ul)"]
+    output = True
+    for name in udf_names:
+        if not artifact.udf.get(name) or artifact.udf.get(name) < 0:
+            output = False
+            LOG.info(
+                f"Sample {artifact.samples[0].id} has an invalid concentration value for {name}. Skipping."
+            )
+    return output
+
+
+@click.command()
+@click.pass_context
+def calculate_saphyr_concentration(ctx) -> None:
+    """Calculates and sets the average concentration and coefficient of variance based on three given concentrations.
+    Returns a message if this worked well, and if there were negative/no/zero concentration values, there's an error message for this
+    """
+
+    LOG.info(f"Running {ctx.command_path} with params: {ctx.params}")
+    process = ctx.obj["process"]
+
+    try:
+        artifacts: List[Artifact] = get_artifacts(process=process, measurement=True)
+        failed_samples = 0
+        for artifact in artifacts:
+            if not validate_udf_values(artifact=artifact):
+                failed_samples += 1
+                continue
+            set_average_and_cv(artifact=artifact)
+        if failed_samples:
+            raise MissingUDFsError(
+                f"{failed_samples} samples have invalid concentration values (<= 0). See log for more information."
+            )
+        message = "The average concentration and coefficient of variance have been calculated for all samples."
+        LOG.info(message)
+        click.echo(message)
+    except LimsError as e:
+        LOG.error(e.message)
+        sys.exit(e.message)