Add project scoring for noncoding regions in SARS-CoV-2, part of #589.

Stop highlighting partial-match contigs as unaligned.
cfe-lab · May 14, 2021 · 1d0bd1a · 1d0bd1a
1 parent 2da6390
commit 1d0bd1a
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Showing 6 changed files with 155 additions and 23 deletions.
diff --git a/micall/core/aln2counts.py b/micall/core/aln2counts.py
@@ -840,7 +840,8 @@ def write_sequence_coverage_counts(self,
             if bead.alignment is not None:
                 cigar = bead.alignment.cigar
             else:
-                cigar = [(bead.end - bead.start, None)]
+                action = CigarActions.MATCH if coordinate_name is None else None
+                cigar = [(bead.end - bead.start, action)]
             for length, action in cigar:
                 if action == CigarActions.DELETE:
                     ref_pos += length

diff --git a/micall/project_scoring.json b/micall/project_scoring.json
@@ -7200,6 +7200,28 @@
     "SARSCOV2": {
       "max_variants": 0,
       "regions": [
+        {
+          "coordinate_region": "SARS-CoV-2-3'UTR",
+          "coordinate_region_length": 226,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-5'UTR",
+          "coordinate_region_length": 262,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
         {
           "coordinate_region": "SARS-CoV-2-E",
           "coordinate_region_length": 75,
@@ -7245,8 +7267,19 @@
           ]
         },
         {
-          "coordinate_region": "SARS-CoV-2-ORF1ab",
-          "coordinate_region_length": 7096,
+          "coordinate_region": "SARS-CoV-2-ORF1a",
+          "coordinate_region_length": 4405,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-ORF1b",
+          "coordinate_region_length": 2695,
           "key_positions": [],
           "min_coverage1": 10,
           "min_coverage2": 50,
@@ -7321,6 +7354,105 @@
             "SARS-CoV-2-seed"
           ]
         },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-1",
+          "coordinate_region_length": 4,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-2",
+          "coordinate_region_length": 5,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-3",
+          "coordinate_region_length": 21,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-4",
+          "coordinate_region_length": 47,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-5",
+          "coordinate_region_length": 7,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-6",
+          "coordinate_region_length": 3,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-7",
+          "coordinate_region_length": 3,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-8",
+          "coordinate_region_length": 11,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
+        {
+          "coordinate_region": "SARS-CoV-2-TRS-B-9",
+          "coordinate_region_length": 21,
+          "key_positions": [],
+          "min_coverage1": 10,
+          "min_coverage2": 50,
+          "min_coverage3": 100,
+          "seed_region_names": [
+            "SARS-CoV-2-seed"
+          ]
+        },
         {
           "coordinate_region": "SARS-CoV-2-nsp1",
           "coordinate_region_length": 179,

diff --git a/micall/tests/test_aln2counts_report.py b/micall/tests/test_aln2counts_report.py
@@ -801,12 +801,12 @@ def test_contig_coverage_report_for_partial_contig(sequence_report):
 
     expected_text = """\
 contig,coordinates,query_nuc_pos,refseq_nuc_pos,dels,coverage,link
-1-R1-seed-partial,,1,1,0,5,U
-1-R1-seed-partial,,2,2,0,5,U
-1-R1-seed-partial,,3,3,0,5,U
-1-R1-seed-partial,,4,4,0,5,U
-1-R1-seed-partial,,5,5,0,5,U
-1-R1-seed-partial,,6,6,0,5,U
+1-R1-seed-partial,,1,1,0,5,M
+1-R1-seed-partial,,2,2,0,5,M
+1-R1-seed-partial,,3,3,0,5,M
+1-R1-seed-partial,,4,4,0,5,M
+1-R1-seed-partial,,5,5,0,5,M
+1-R1-seed-partial,,6,6,0,5,M
 """
 
     report_file = StringIO()
@@ -835,12 +835,12 @@ def test_contig_coverage_report_for_reversed_contig(sequence_report):
 
     expected_text = """\
 contig,coordinates,query_nuc_pos,refseq_nuc_pos,dels,coverage,link
-1-R1-seed-reversed,,1,1,0,5,U
-1-R1-seed-reversed,,2,2,0,5,U
-1-R1-seed-reversed,,3,3,0,5,U
-1-R1-seed-reversed,,4,4,0,5,U
-1-R1-seed-reversed,,5,5,0,5,U
-1-R1-seed-reversed,,6,6,0,5,U
+1-R1-seed-reversed,,1,1,0,5,M
+1-R1-seed-reversed,,2,2,0,5,M
+1-R1-seed-reversed,,3,3,0,5,M
+1-R1-seed-reversed,,4,4,0,5,M
+1-R1-seed-reversed,,5,5,0,5,M
+1-R1-seed-reversed,,6,6,0,5,M
 """
 
     report_file = StringIO()

diff --git a/micall/tests/test_denovo.py b/micall/tests/test_denovo.py
@@ -1,7 +1,7 @@
 from io import StringIO
 from pathlib import Path
 
-from pytest import fixture
+from pytest import fixture, mark
 
 from micall.core.denovo import write_contig_refs, denovo, DEFAULT_DATABASE, genotype
 from micall.blast_db.make_blast_db import make_blast_db, DEFAULT_PROJECTS
@@ -207,6 +207,7 @@ def test_merged_contig(tmpdir, hcv_db):
     assert expected_contigs_csv == contigs_csv.getvalue()
 
 
+@mark.iva()
 def test_denovo_iva(tmpdir, hcv_db):
     microtest_path = Path(__file__).parent / 'microtest'
     contigs_csv = StringIO()
@@ -221,8 +222,8 @@ def test_denovo_iva(tmpdir, hcv_db):
 AGGCGGTGATGGGGGCTTCTTATGGATTCCAGTACTCCC
 """
 
-    denovo(microtest_path / '2160A-HCV_S19_L001_R1_001.fastq',
-           microtest_path / '2160A-HCV_S19_L001_R2_001.fastq',
+    denovo(str(microtest_path / '2160A-HCV_S19_L001_R1_001.fastq'),
+           str(microtest_path / '2160A-HCV_S19_L001_R2_001.fastq'),
            contigs_csv,
            tmpdir)
 

diff --git a/micall/tests/test_plot_contigs.py b/micall/tests/test_plot_contigs.py
@@ -115,7 +115,7 @@ def drawing_to_image(drawing: Drawing) -> Image:
     return image
 
 
-def encode_image(image: Image) -> bytes:
+def encode_image(image: Image) -> str:
     writer = BytesIO()
     image.save(writer, format='PNG')
     encoded = standard_b64encode(writer.getvalue())

diff --git a/pytest.ini b/pytest.ini
@@ -1,5 +1,3 @@
 [pytest]
-norecursedirs = sandbox
-
-# Can remove this filter when BioPython upgrades to 1.78.
-filterwarnings = ignore::PendingDeprecationWarning:Bio.Alphabet
+markers =
+    iva: test requires IVA (deselect with '-m "not iva"')