Merge pull request #70 from GavinHuttley/develop

basic test of writing alignments

noxfile.py

@@ -12,8 +12,6 @@ def test(session):
         "pytest",
         "-s",
         "-x",
-        "-m",
-        "not slow",
         "--cov-report",
         f"lcov:lcov-{session.python}.info",
         "--cov",

src/ensembl_lite/_aligndb.py

@@ -455,12 +455,13 @@ def write_alignments(
     outdir: os.PathLike,
     ref_species: str,
     stableids: list[str],
+    show_progress: bool = True,
 ):
     # then the coordinates for the id's
     ref_genome = genomes[ref_species]
     locations = []
     for stableid in stableids:
-        record = list(ref_genome.annotations.get_records_matching(name=stableid))
+        record = list(ref_genome.annotation_db.get_records_matching(name=stableid))
         if not record:
             continue
         elif len(record) == 1:
@@ -478,7 +479,9 @@ def write_alignments(
     if limit:
         locations = locations[:limit]
 
-    for stableid, species, seqid, start, end in track(locations):
+    for stableid, species, seqid, start, end in track(
+        locations, disable=not show_progress
+    ):
         alignments = list(
             get_alignment(
                 align_db,

tests/test_aligndb.py

@@ -3,14 +3,15 @@
 import numpy
 import pytest
 
-from cogent3 import make_seq
+from cogent3 import load_aligned_seqs, make_seq
 from cogent3.core.annotation_db import GffAnnotationDb
 
 from ensembl_lite._aligndb import (
     AlignDb,
     AlignRecord,
     GapPositions,
     get_alignment,
+    write_alignments,
 )
 from ensembl_lite._genomedb import CompressedGenomeSeqsDb, Genome
 from ensembl_lite.convert import seq_to_gap_coords
@@ -578,3 +579,20 @@ def test_align_db_get_records_no_matches(coord):
 def test_get_species():
     _, align_db = make_sample()
     assert set(align_db.get_species_names()) == {"dog", "human", "mouse"}
+
+
+def test_write_alignments(tmp_path):
+    genomes, align_db = make_sample(two_aligns=True)
+    write_alignments(
+        align_db=align_db,
+        genomes=genomes,
+        outdir=tmp_path,
+        limit=None,
+        mask_features=None,
+        stableids=["not-on-s2"],
+        ref_species="human",
+        show_progress=False,
+    )
+    aln_path = list(tmp_path.glob("*"))[0]
+    aln = load_aligned_seqs(aln_path, moltype="dna")
+    assert len(aln) == 3