From e1f6581a817034cf38a8b6a091741a3b0a2e86e8 Mon Sep 17 00:00:00 2001
From: AroneyS <samuel.aroney@qut.edu.au>
Date: Thu, 2 May 2024 08:30:49 +1000
Subject: [PATCH] add dtypes to evaluate.py inputs
---
binchicken.yml | 2 +-
binchicken/workflow/scripts/evaluate.py | 43 +++++++++++++++++++++----
2 files changed, 38 insertions(+), 7 deletions(-)
diff --git a/binchicken.yml b/binchicken.yml
index 24446a50..02fda45e 100644
--- a/binchicken.yml
+++ b/binchicken.yml
@@ -11,7 +11,7 @@ dependencies:
- bird_tool_utils_python=0.4.*
- extern=0.4.*
- ruamel.yaml=0.17.*
- - polars=0.20.*
+ - polars=0.20.4
- pigz=2.3.*
- pyarrow=12.0.*
- parallel=20230522
diff --git a/binchicken/workflow/scripts/evaluate.py b/binchicken/workflow/scripts/evaluate.py
index 2f2d33b2..41985189 100755
--- a/binchicken/workflow/scripts/evaluate.py
+++ b/binchicken/workflow/scripts/evaluate.py
@@ -6,7 +6,38 @@
import polars as pl
import os
-OUTPUT_COLUMNS={
+SINGLEM_COLUMNS = {
+ "gene": str,
+ "sample": str,
+ "sequence": str,
+ "num_hits": int,
+ "coverage": float,
+ "taxonomy": str,
+}
+
+TARGET_COLUMNS = SINGLEM_COLUMNS | {
+ "target": int,
+}
+APPRAISE_COLUMNS = SINGLEM_COLUMNS | {
+ "found_in": str,
+}
+
+CLUSTER_COLUMNS = {
+ "samples": str,
+ "length": int,
+ "total_targets": int,
+ "total_size": int,
+ "recover_samples": str,
+ "coassembly": str,
+}
+EDGE_COLUMNS = {
+ "style": str,
+ "cluster_size": int,
+ "samples": str,
+ "target_ids": str,
+}
+
+OUTPUT_COLUMNS = {
"coassembly": str,
"gene": str,
"sequence": str,
@@ -302,11 +333,11 @@ def summarise_stats(matches, combined_otu_table, recovered_bins):
novel_hits_path = snakemake.output.novel_hits
summary_stats_path = snakemake.output.summary_stats
- target_otu_table = pl.read_csv(target_path, separator="\t")
- binned_otu_table = pl.read_csv(binned_path, separator="\t")
- elusive_clusters = pl.read_csv(elusive_clusters_path, separator="\t")
- elusive_edges = pl.read_csv(elusive_edges_path, separator="\t")
- recovered_otu_table = pl.read_csv(recovered_otu_table_path, separator="\t")
+ target_otu_table = pl.read_csv(target_path, separator="\t", dtypes=TARGET_COLUMNS)
+ binned_otu_table = pl.read_csv(binned_path, separator="\t", dtypes=APPRAISE_COLUMNS)
+ elusive_clusters = pl.read_csv(elusive_clusters_path, separator="\t", dtypes=CLUSTER_COLUMNS)
+ elusive_edges = pl.read_csv(elusive_edges_path, separator="\t", dtypes=EDGE_COLUMNS)
+ recovered_otu_table = pl.read_csv(recovered_otu_table_path, separator="\t", dtypes=SINGLEM_COLUMNS)
matches, unmatched, summary = evaluate(target_otu_table, binned_otu_table, elusive_clusters, elusive_edges, recovered_otu_table, recovered_bins)
# Export hits matching elusive targets