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In Anglerfish parsing, only assign barcode-specific UDFs to barcoded samples #306

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Feb 9, 2024
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In Anglerfish parsing, only assign barcode-specific UDFs to barcoded samples #306

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4 changes: 4 additions & 0 deletions VERSIONLOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# Scilifelab_epps Version Log

## 20240208.1

In Anglerfish parsing, only try to assign barcode-specific UDFs for barcoded samples.

## 20240130.1

Handle Anglerfish result parsing for runs W/O ONT barcodes
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22 changes: 13 additions & 9 deletions scripts/parse_anglerfish_results.py
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Expand Up @@ -114,15 +114,6 @@ def ont_barcode_well2name(barcode_well: str) -> str:


def fill_udfs(currentStep: Process, df: pd.DataFrame):
# Dictate which LIMS UDF corresponds to which column in the dataframe
udfs_to_cols = {
"# Reads": "num_reads",
"Avg. Read Length": "mean_read_len",
"Std. Read Length": "std_read_len",
"Representation Within Run (%)": "repr_total_pc",
"Representation Within Barcode (%)": "repr_within_barcode_pc",
}

# Get Illumina pools
illumina_pools = [
input_art
Expand Down Expand Up @@ -160,12 +151,25 @@ def fill_udfs(currentStep: Process, df: pd.DataFrame):
]

else:
# Subset df to the current Illumina sample
df_sample = df[df["sample_name"] == illumina_sample.name]

assert (
len(df_sample) == 1
), f"Multiple entries matching both Illumina sample name {illumina_sample.name} and ONT barcode {barcode_name} was found in the dataframe."

# Determine which UDFs to assign
udfs_to_cols = {
"# Reads": "num_reads",
"Avg. Read Length": "mean_read_len",
"Std. Read Length": "std_read_len",
"Representation Within Run (%)": "repr_total_pc",
}
if barcode_well:
udfs_to_cols[
"Representation Within Barcode (%)"
] = "repr_within_barcode_pc"

# Start putting UDFs
for udf, col in udfs_to_cols.items():
try:
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