Fix tests and drop donut plot scaffolding

Author: standage

docs/cli.md

@@ -75,16 +75,6 @@ In brief, this means that every stable version of the MicroHapulator software is
 :nodefault:
 ```
 
-### `mhpl8r mappingqc`
-```{argparse}
-:module: microhapulator.cli
-:func: get_parser
-:prog: mhpl8r
-:path: mappingqc
-:nodefault:
-```
-
-
 ### `mhpl8r contrib`
 
 ```{argparse}

microhapulator/api.py

@@ -815,30 +815,14 @@ def consolidate_read_mapping_qc_tables(samples):
     return aggregate_qc_table
 
 
-def read_mapping_qc(marker_mapped, refr_mapped, repetitive_mapped, figure=None, title=None):
+def read_mapping_qc(marker_mapped, refr_mapped, repetitive_mapped):
     """Count on target, off target, repetitive, and contaminant reads
 
     :param str marker_mapped: path of txt file containing number of reads mapped to marker sequences
     :param str refr_mapped: path of txt file containing number of reads mapped to the full human reference genome
     :param str repetitive_mapped: path of txt file containing number of reads mapped preferentially to non-marker loci in the human reference genome
-    :param str output: path where the png file of the plot will be saved
-    :param str sample: name of the sample to be included as the plot title; by default no sample name is shown
     """
-    data = count_mapped_read_types(marker_mapped, refr_mapped, repetitive_mapped)
-    if not figure:
-        return data
-    backend = matplotlib.get_backend()
-    plt.switch_backend("Agg")
-    labels = ["on target", "off target", "contamination", "repetitive"]
-    plt.pie(data.values[0])
-    circle = plt.Circle((0, 0), 0.7, color="white")
-    plt.gca().add_artist(circle)
-    plt.title(title, fontsize=14)
-    plt.legend(labels=labels[: len(data.values[0])], bbox_to_anchor=(1.05, 1.0), loc="upper left")
-    plt.savefig(figure, bbox_inches="tight", dpi=300)
-    plt.close("all")
-    plt.switch_backend(backend)
-    return data
+    return count_mapped_read_types(marker_mapped, refr_mapped, repetitive_mapped)
 
 
 def count_mapped_read_types(marker_mapped, refr_mapped, repetitive_mapped):

microhapulator/cli/__init__.py

@@ -22,7 +22,6 @@
 from . import getrefr
 from . import hetbalance
 from . import locbalance
-from . import mappingqc
 from . import mix
 from . import repetitive
 from . import pipe
@@ -43,7 +42,6 @@
     "getrefr": getrefr.main,
     "hetbalance": hetbalance.main,
     "locbalance": locbalance.main,
-    "mappingqc": mappingqc.main,
     "mix": mix.main,
     "repetitive": repetitive.main,
     "pipe": pipe.main,
@@ -64,7 +62,6 @@
     "getrefr": getrefr.subparser,
     "hetbalance": hetbalance.subparser,
     "locbalance": locbalance.subparser,
-    "mappingqc": mappingqc.subparser,
     "mix": mix.subparser,
     "repetitive": repetitive.subparser,
     "pipe": pipe.subparser,

microhapulator/cli/mappingqc.py

@@ -10,8 +10,10 @@
 # Development Center.
 # -------------------------------------------------------------------------------------------------
 
+import microhapulator.api as mhapi
 from microhapulator.pipe.mapstats import MappingStats, MappingSummary
 from microhapulator.tests import data_file
+import pandas as pd
 import pytest
 
 
@@ -37,3 +39,14 @@ def test_load_mapsummary_from_workdir():
     assert repetitive["mh17KK-278.v1"]["SRM8398-1"].repetitive == 0
     assert repetitive["mh17KK-278.v1"]["SRM8398-2"].repetitive == 0
     assert repetitive["mh17KK-278.v1"]["SRM8398-3"].repetitive == 0
+
+
+def test_mappingqc(tmp_path):
+    align_dir = data_file("mapping_workdir/analysis/SRM8398-2/02alignment/")
+    obs_data = mhapi.read_mapping_qc(
+        f"{align_dir}/SRM8398-2.bam.stats",
+        f"{align_dir}/fullrefr/SRM8398-2-fullrefr-mapped-reads.txt",
+        f"{align_dir}/SRM8398-2-repetitive-reads.csv",
+    )
+    exp_data = pd.read_csv(data_file("test-mapping-qc.csv"))
+    assert obs_data.equals(exp_data)

microhapulator/tests/test_mapstats.py microhapulator/tests/test_mapping.pymicrohapulator/tests/test_mapstats.py renamed to microhapulator/tests/test_mapping.py

@@ -303,10 +303,9 @@ rule read_mapping_qc:
         repetitive=rules.repetitive_mapping.output.counts,
     output:
         counts="analysis/{sample}/02alignment/{sample}-read-mapping-qc.csv",
-    shell:
-        """
-        mhpl8r mappingqc {input.marker} {input.full_refr} {input.repetitive} --csv {output.counts}
-        """
+    run:
+        results = mhapi.read_mapping_qc(input.marker, input.full_refr, input.repetitive)
+        results.to_csv(output.counts, index=False)
 
 
 rule aggregate_read_mapping_qc: