test: bolster align tests (#12)

misc/bug_hunting/check_align.py

@@ -0,0 +1,56 @@
+import logging
+import pickle
+
+from cool_seq_tool.schemas import Strand
+
+from dcd_mapping.align import align
+from dcd_mapping.resources import LOCAL_STORE_PATH, get_scoreset_metadata
+
+logging.basicConfig(
+    filename="dcd-check-align.log",
+    format="%(asctime)s %(levelname)s:%(name)s:%(message)s",
+    level=logging.WARNING,
+    force=True,
+)
+
+_logger = logging.getLogger(__name__)
+
+with open("notebooks/analysis/results/mave_blat.pickle", "rb") as f:
+    mave_blat_dict = pickle.load(f)
+
+with open(LOCAL_STORE_PATH / "human_urns.txt", "r") as f:
+    urns = [line.strip() for line in f.readlines()]
+
+strand_reformat = {1: Strand.POSITIVE, -1: Strand.NEGATIVE}
+
+
+def format_chrom(chrom):
+    return f"chr{chrom}"
+
+
+for urn in urns:
+    print(f"Checking {urn}...")
+    try:
+        metadata = get_scoreset_metadata(urn)
+        alignment = align(metadata, False, True)
+    except Exception as e:
+        _logger.error("%s error: %s", urn, e)
+        continue
+    if urn not in mave_blat_dict:
+        continue
+    original = mave_blat_dict[urn]
+    try:
+        for name, actual, expected in [
+            ("chromosome", alignment.chrom, format_chrom(original["chrom"])),
+            ("strand", alignment.strand, strand_reformat[original["strand"]]),
+        ]:
+            if actual != expected:
+                _logger.error(
+                    "%s %s mismatch: %s (actual) vs %s (expected)",
+                    urn,
+                    name,
+                    actual,
+                    expected,
+                )
+    except Exception as e:
+        _logger.error("%s exception: %s", urn, e)

pyproject.toml

@@ -73,6 +73,7 @@ branch = true
 
 [tool.ruff]
 src = ["src"]
+exclude = ["misc/*"]
 # pycodestyle (E, W)
 # Pyflakes (F)
 # flake8-annotations (ANN)

tests/conftest.py

@@ -1,4 +1,11 @@
-"""Provide shared testing utilities."""
+"""Provide shared testing utilities.
+
+
+Notes on test cases:
+-------------------
+
+* urn:mavedb:00000068-a-1: TP53, protein-coding, DNA.
+"""
 import json
 import os
 from pathlib import Path

tests/fixtures/align_result.json

@@ -58,5 +58,37 @@
       { "start": 1261199, "end": 12612062 },
       { "start": 12618514, "end": 12618568 }
     ]
+  },
+  "urn:mavedb:00000068-a-1": {
+    "chrom": "chr17",
+    "strand": -1,
+    "coverage": 99.83079526226734,
+    "ident_pct": 99.91525423728814,
+    "query_range": { "start": 0, "end": 1180 },
+    "query_subranges": [
+      { "start": 1100, "end": 1180 },
+      { "start": 993, "end": 1100 },
+      { "start": 919, "end": 993 },
+      { "start": 782, "end": 919 },
+      { "start": 672, "end": 782 },
+      { "start": 559, "end": 672 },
+      { "start": 375, "end": 559 },
+      { "start": 96, "end": 375 },
+      { "start": 74, "end": 96 },
+      { "start": 0, "end": 74 }
+    ],
+    "hit_range": { "start": 7676520, "end": 7669690 },
+    "hit_subranges": [
+      { "start": 7669610, "end": 7669690 },
+      { "start": 7670608, "end": 7670715 },
+      { "start": 7673534, "end": 7673608 },
+      { "start": 7673700, "end": 7673837 },
+      { "start": 7674180, "end": 7674290 },
+      { "start": 7674858, "end": 7674971 },
+      { "start": 7675052, "end": 7675236 },
+      { "start": 7675993, "end": 7676272 },
+      { "start": 7676381, "end": 7676403 },
+      { "start": 7676520, "end": 7676594 }
+    ]
   }
 }

tests/fixtures/scoreset_metadata.json

@@ -62,6 +62,15 @@
       "target_sequence_type": "dna",
       "target_reference_genome": "hg38",
       "target_uniprot_ref": { "id": "uniprot:P04049", "offset": 51 }
+    },
+    {
+      "urn": "urn:mavedb:00000068-a-1",
+      "target_gene_name": "TP53 (P72R)",
+      "target_gene_category": "Protein coding",
+      "target_sequence": "ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTAG",
+      "target_sequence_type": "dna",
+      "target_reference_genome": "hg38",
+      "target_uniprot_ref": null
     }
   ]
 }

tests/fixtures/urn:mavedb:00000068-a-1_scores.csv

@@ -0,0 +1,48 @@
+accession,hgvs_nt,hgvs_splice,hgvs_pro,score
+urn:mavedb:00000068-a-1#528,NA,NA,p.Gly389Ter,-0.8448754497234633
+urn:mavedb:00000068-a-1#546,NA,NA,p.Gly389Cys,-0.5081453414881882
+urn:mavedb:00000068-a-1#612,NA,NA,p.His365Ter,-2.226787236679561
+urn:mavedb:00000068-a-1#547,NA,NA,p.Gly389=,-0.3114032004197305
+urn:mavedb:00000068-a-1#613,NA,NA,p.His365Tyr,-0.36585451364742
+urn:mavedb:00000068-a-1#548,NA,NA,p.Gly389Ala,-0.8482077472283238
+urn:mavedb:00000068-a-1#549,NA,NA,p.Glu388Ter,0.05530191813883238
+urn:mavedb:00000068-a-1#550,NA,NA,p.Glu388Tyr,-0.34329774205619
+urn:mavedb:00000068-a-1#551,NA,NA,p.Glu388Trp,-1.5238647488862949
+urn:mavedb:00000068-a-1#552,NA,NA,p.Glu388Val,-0.6422615384883972
+urn:mavedb:00000068-a-1#553,NA,NA,p.Glu388Thr,-0.8490660813565178
+urn:mavedb:00000068-a-1#554,NA,NA,p.Glu388Ser,-1.2839487661086697
+urn:mavedb:00000068-a-1#555,NA,NA,p.Glu388Arg,-1.024302690973422
+urn:mavedb:00000068-a-1#556,NA,NA,p.Glu388Gln,-0.3114282471795208
+urn:mavedb:00000068-a-1#557,NA,NA,p.Glu388Pro,-0.5571635356150665
+urn:mavedb:00000068-a-1#558,NA,NA,p.Glu388Asn,-0.5151230575285044
+urn:mavedb:00000068-a-1#559,NA,NA,p.Glu388Met,-1.2506258908030141
+urn:mavedb:00000068-a-1#614,NA,NA,p.His365Trp,-1.1230151778981163
+urn:mavedb:00000068-a-1#560,NA,NA,p.Glu388Leu,-0.6969258713954155
+urn:mavedb:00000068-a-1#615,NA,NA,p.His365Val,-0.826647313158234
+urn:mavedb:00000068-a-1#561,NA,NA,p.Glu388Lys,0.044449447270876415
+urn:mavedb:00000068-a-1#562,NA,NA,p.Glu388Ile,-0.6703081212668602
+urn:mavedb:00000068-a-1#616,NA,NA,p.His365Thr,-1.2339323429418732
+urn:mavedb:00000068-a-1#563,NA,NA,p.Glu388His,-1.0228758006971406
+urn:mavedb:00000068-a-1#617,NA,NA,p.His365Ser,-1.207958290024986
+urn:mavedb:00000068-a-1#564,NA,NA,p.Glu388Gly,0.1928432362603335
+urn:mavedb:00000068-a-1#565,NA,NA,p.Glu388Phe,-0.7995695025755253
+urn:mavedb:00000068-a-1#566,NA,NA,p.Glu388Asp,-0.5734467636981624
+urn:mavedb:00000068-a-1#567,NA,NA,p.Glu388Cys,-0.5200106027473981
+urn:mavedb:00000068-a-1#618,NA,NA,p.His365Arg,-0.15648499129119786
+urn:mavedb:00000068-a-1#568,NA,NA,p.Glu388=,0.13439466320551569
+urn:mavedb:00000068-a-1#569,NA,NA,p.Glu388Ala,-0.24796460732041514
+urn:mavedb:00000068-a-1#595,NA,NA,p.Ser366Tyr,-0.11899995564102445
+urn:mavedb:00000068-a-1#596,NA,NA,p.Ser366Trp,-1.419503452209785
+urn:mavedb:00000068-a-1#597,NA,NA,p.Ser366Val,-0.38831518205082655
+urn:mavedb:00000068-a-1#598,NA,NA,p.Ser366Thr,-0.843833245301256
+urn:mavedb:00000068-a-1#599,NA,NA,p.Ser366Arg,-0.6638684644018105
+urn:mavedb:00000068-a-1#600,NA,NA,p.Ser366Gln,-0.4299226799331797
+urn:mavedb:00000068-a-1#601,NA,NA,p.Ser366Pro,-0.5476098144406847
+urn:mavedb:00000068-a-1#602,NA,NA,p.Ser366Lys,-1.1512867723916729
+urn:mavedb:00000068-a-1#603,NA,NA,p.Ser366Ile,-0.6304135202423646
+urn:mavedb:00000068-a-1#604,NA,NA,p.Ser366His,-1.1104041758877286
+urn:mavedb:00000068-a-1#605,NA,NA,p.Ser366Gly,-0.5861940789803509
+urn:mavedb:00000068-a-1#606,NA,NA,p.Ser366Phe,-0.1552908998376018
+urn:mavedb:00000068-a-1#607,NA,NA,p.Ser366Glu,-0.8533090945531668
+urn:mavedb:00000068-a-1#608,NA,NA,p.Ser366Asp,-1.3609765742847353
+urn:mavedb:00000068-a-1#609,NA,NA,p.Ser366Cys,-1.6901296514759063