loqusdb 2.7.19__tar.gz → 2.7.21__tar.gz

{loqusdb-2.7.19 → loqusdb-2.7.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.19
+Version: 2.7.21
 Summary: A simple observation count database
 License: MIT
 Author: Your Name

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.19"
+__version__ = "2.7.21"
 
 INDEXES = {
     "variant": [
@@ -61,32 +61,3 @@ INDEXES = {
         ),
     ],
 }
-
-CHROMOSOME_ORDER = (
-    "1",
-    "2",
-    "3",
-    "4",
-    "5",
-    "6",
-    "7",
-    "8",
-    "9",
-    "10",
-    "11",
-    "12",
-    "13",
-    "14",
-    "15",
-    "16",
-    "17",
-    "18",
-    "19",
-    "20",
-    "21",
-    "22",
-    "23",
-    "X",
-    "Y",
-    "MT",
-)

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/build_models/variant.py

@@ -15,18 +15,17 @@ Position = namedtuple("Position", "chrom pos")
 # These are coordinate for the pseudo autosomal regions in GRCh37
 
 
-def check_par(chrom, pos, genome_build=None):
+def check_par(chrom, pos, genome_build):
     """Check if a coordinate is in the PAR region
 
     Args:
         chrom(str)
         pos(int)
+        genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
     Returns:
         par(bool)
     """
-    if genome_build is None:
-        genome_build = GRCH37
     return any(
         pos >= interval[0] and pos <= interval[1] for interval in PAR[genome_build].get(chrom, [])
     )
@@ -50,24 +49,25 @@ def get_variant_id(variant, keep_chr_prefix=None):
     return "_".join([str(chrom), str(variant.POS), str(variant.REF), str(variant.ALT[0])])
 
 
-def is_greater(a, b):
+def is_greater(a, b, genome_build):
     """Check if position a is greater than position b
     This will look at chromosome and position.
 
     For example a position where chrom = 2 and pos = 300 is greater than a position where
     chrom = 1 and pos = 1000
 
-    If any of the chromosomes is outside [1-22,X,Y,MT] we can not say which is biggest.
+    If any of the chromosomes is outside [1-22,X,Y,MT] or [chr1-chr22,chrX,chrY,chrM] we can not say which is biggest.
 
     Args:
         a,b(Position)
+        genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
     Returns:
         bool: True if a is greater than b
     """
 
-    a_chrom = CHROM_TO_INT.get(a.chrom, 0)
-    b_chrom = CHROM_TO_INT.get(b.chrom, 0)
+    a_chrom = CHROM_TO_INT[genome_build].get(a.chrom, 0)
+    b_chrom = CHROM_TO_INT[genome_build].get(b.chrom, 0)
 
     if a_chrom == 0 or b_chrom == 0:
         return False
@@ -78,12 +78,13 @@ def is_greater(a, b):
     return a_chrom == b_chrom and a.pos > b.pos
 
 
-def get_coords(variant, keep_chr_prefix):
+def get_coords(variant, keep_chr_prefix, genome_build):
     """Returns a dictionary with position information
 
     Args:
         variant(cyvcf2.Variant)
         keep_chr_prefix(bool): Retain chr/CHR/Chr prefix when present
+        genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
     Returns:
         coordinates(dict)
@@ -139,7 +140,7 @@ def get_coords(variant, keep_chr_prefix):
     end_position = Position(end_chrom, end)
 
     # If 'start' is greater than 'end', switch positions
-    if is_greater(position, end_position):
+    if is_greater(position, end_position, genome_build=genome_build):
         end_chrom = position.chrom
         end = position.pos
 
@@ -201,7 +202,7 @@ def build_variant(
     # We allways assume splitted and normalized VCFs
     alt = variant.ALT[0]
 
-    coordinates = get_coords(variant, keep_chr_prefix)
+    coordinates = get_coords(variant, keep_chr_prefix, genome_build=genome_build)
     chrom = coordinates["chrom"]
     pos = coordinates["pos"]
 
@@ -239,7 +240,7 @@ def build_variant(
                 # If variant in X or Y and individual is male,
                 # we need to check hemizygosity
                 if (
-                    chrom in ["X", "Y"]
+                    chrom in ["X", "Y", "chrX", "chrY"]
                     and ind_obj["sex"] == 1
                     and not check_par(chrom, pos, genome_build=genome_build)
                 ):

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/commands/cli.py

@@ -52,6 +52,8 @@ LOG = logging.getLogger(__name__)
 @click.option(
     "-g",
     "--genome-build",
+    default="GRCh37",
+    show_default=True,
     type=click.Choice([GRCH37, GRCH38]),
     help="Specify what genome build to use",
 )
@@ -121,7 +123,7 @@ def cli(
 
     adapter = MongoAdapter(client, db_name=database)
 
-    genome_build = genome_build or configs.get("genome_build") or GRCH37
+    genome_build = genome_build or configs.get("genome_build")
     keep_chr_prefix = keep_chr_prefix or configs.get("keep_chr_prefix")
 
     ctx.obj = {}

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/commands/export.py

@@ -2,7 +2,7 @@ import logging
 from datetime import datetime
 
 import click
-from loqusdb import CHROMOSOME_ORDER
+from loqusdb.constants import CHROMOSOMES, GRCH37, GRCH38
 from loqusdb.utils.variant import format_variant
 from vcftoolbox import HeaderParser, print_headers, print_variant
 
@@ -43,11 +43,22 @@ def export(ctx, outfile, variant_type, freq):
     is_sv = variant_type == "sv"
     existing_chromosomes = set(adapter.get_chromosomes(sv=is_sv))
 
+    genome = ctx.obj["genome_build"]
+    chromosome_order = CHROMOSOMES[genome]
+    keep_chr_prefix = ctx.obj["keep_chr_prefix"]
+
     ordered_chromosomes = []
-    for chrom in CHROMOSOME_ORDER:
-        if chrom in existing_chromosomes:
+    for chrom in chromosome_order:
+        if keep_chr_prefix and chrom in existing_chromosomes:
             ordered_chromosomes.append(chrom)
             existing_chromosomes.remove(chrom)
+        elif not keep_chr_prefix:
+            if genome == GRCH37 and chrom in existing_chromosomes:
+                ordered_chromosomes.append(chrom)
+                existing_chromosomes.remove(chrom)
+            elif genome == GRCH38 and chrom[3:] in existing_chromosomes:
+                ordered_chromosomes.append(chrom)
+                existing_chromosomes.remove(chrom)
     for chrom in existing_chromosomes:
         ordered_chromosomes.append(chrom)
 

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/commands/view.py

@@ -117,16 +117,40 @@ def variants(
             sv_cases = True
         nr_cases = adapter.nr_cases(snv_cases=snv_cases, sv_cases=sv_cases)
 
+    if chromosome:
+        if chromosome.startswith("chr"):
+            chromosomes = [chromosome, chromosome[3:]]
+        elif not chromosome.startswith("chr"):
+            chromosomes = [chromosome, "chr" + chromosome]
+
+    if end_chromosome:
+        if end_chromosome.startswith("chr"):
+            end_chromosomes = [end_chromosome, end_chromosome[3:]]
+        elif not end_chromosome.startswith("chr"):
+            end_chromosomes = [end_chromosome, "chr" + end_chromosome]
+    else:
+        end_chromosomes = [None, None]
+
     if variant_id:
         if variant_type == "sv":
             variant_query = {
-                "chrom": chromosome,
-                "end_chrom": end_chromosome or chromosome,
+                "chrom": chromosomes[0],
+                "end_chrom": end_chromosomes[0] or chromosomes[0],
                 "sv_type": sv_type,
                 "pos": start,
                 "end": end,
             }
-            variant = adapter.get_structural_variant(variant_query)
+            variant = list(adapter.get_structural_variant(variant_query))
+            if len(variant) == 0:
+                variant_query = {
+                    "chrom": chromosomes[1],
+                    "end_chrom": end_chromosomes[1] or chromosomes[1],
+                    "sv_type": sv_type,
+                    "pos": start,
+                    "end": end,
+                }
+                variant = adapter.get_structural_variant(variant_query)
+
         else:
             variant = adapter.get_variant({"_id": variant_id})
 
@@ -145,18 +169,29 @@ def variants(
 
         click.echo(variant)
         return
-
     if variant_type == "snv":
-        result = adapter.get_variants(chromosome=chromosome, start=start, end=end)
+        result = list(adapter.get_variants(chromosome=chromosomes[0], start=start, end=end))
+        if len(result) == 0:
+            result = adapter.get_variants(chromosome=chromosomes[1], start=start, end=end)
     else:
         LOG.info("Search for svs")
-        result = adapter.get_sv_variants(
-            chromosome=chromosome,
-            end_chromosome=end_chromosome,
-            sv_type=sv_type,
-            pos=start,
-            end=end,
+        result = list(
+            adapter.get_sv_variants(
+                chromosome=chromosomes[0],
+                end_chromosome=end_chromosomes[0],
+                sv_type=sv_type,
+                pos=start,
+                end=end,
+            )
         )
+        if len(result) == 0:
+            result = adapter.get_sv_variants(
+                chromosome=chromosomes[1],
+                end_chromosome=end_chromosomes[1],
+                sv_type=sv_type,
+                pos=start,
+                end=end,
+            )
 
     if to_json:
         json.dumps(variant)

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/constants/__init__.py

@@ -17,35 +17,67 @@ PAR = {
 GENOTYPE_MAP = {0: "hom_ref", 1: "het", 2: "no_call", 3: "hom_alt"}
 
 # To keep the order of chromosomes
-CHROMOSOMES = (
-    "1",
-    "2",
-    "3",
-    "4",
-    "5",
-    "6",
-    "7",
-    "8",
-    "9",
-    "10",
-    "11",
-    "12",
-    "13",
-    "14",
-    "15",
-    "16",
-    "17",
-    "18",
-    "19",
-    "20",
-    "21",
-    "22",
-    "X",
-    "Y",
-    "MT",
-)
+CHROMOSOMES = {
+    GRCH37: [
+        "1",
+        "2",
+        "3",
+        "4",
+        "5",
+        "6",
+        "7",
+        "8",
+        "9",
+        "10",
+        "11",
+        "12",
+        "13",
+        "14",
+        "15",
+        "16",
+        "17",
+        "18",
+        "19",
+        "20",
+        "21",
+        "22",
+        "X",
+        "Y",
+        "MT",
+    ],
+    GRCH38: [
+        "chr1",
+        "chr2",
+        "chr3",
+        "chr4",
+        "chr5",
+        "chr6",
+        "chr7",
+        "chr8",
+        "chr9",
+        "chr10",
+        "chr11",
+        "chr12",
+        "chr13",
+        "chr14",
+        "chr15",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr20",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY",
+        "chrM",
+    ],
+}
 
-CHROM_TO_INT = {chrom: i + 1 for i, chrom in enumerate(CHROMOSOMES)}
+CHROM_TO_INT = {
+    build: {chrom: i + 1 for i, chrom in enumerate(chromosomes)}
+    for build, chromosomes in CHROMOSOMES.items()
+}
 
 # Ranges of hamming distances to be checked when 'loqusdb profile --stats'
 # items:   <range_name>: <range>

{loqusdb-2.7.19 → loqusdb-2.7.21}/loqusdb/utils/delete.py

@@ -21,6 +21,7 @@ def delete(
         existing_case(models.Case): If something failed during an update we need to revert
                                     to the original case
         keep_chr_prefix(bool): Retain chr/CHR/Chr prefixes in chromosome IDs when they are present
+        genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
     """
     # This will overwrite the updated case with the previous one
@@ -48,7 +49,11 @@ def delete(
         elif file_type == "vcf_sv_path":
             LOG.info("deleting structural variants")
             delete_structural_variants(
-                adapter=adapter, vcf_obj=vcf_obj, case_obj=case_obj, keep_chr_prefix=keep_chr_prefix
+                adapter=adapter,
+                vcf_obj=vcf_obj,
+                case_obj=case_obj,
+                keep_chr_prefix=keep_chr_prefix,
+                genome_build=genome_build,
             )
 
 
@@ -62,6 +67,7 @@ def delete_variants(
         vcf_obj(iterable(dict))
         ind_positions(dict)
         case_id(str)
+        genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
     Returns:
         nr_deleted (int): Number of deleted variants
@@ -120,7 +126,9 @@ def delete_variants(
     return nr_deleted
 
 
-def delete_structural_variants(adapter, vcf_obj, case_obj, keep_chr_prefix=None, case_id=None):
+def delete_structural_variants(
+    adapter, vcf_obj, case_obj, genome_build, keep_chr_prefix=None, case_id=None
+):
     """Delete structural variants for a case in the database
 
     Args:
@@ -128,6 +136,7 @@ def delete_structural_variants(adapter, vcf_obj, case_obj, keep_chr_prefix=None,
         vcf_obj(iterable(dict))
         ind_positions(dict)
         case_id(str)
+        genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
     Returns:
         nr_deleted (int): Number of deleted variants"""
@@ -141,7 +150,11 @@ def delete_structural_variants(adapter, vcf_obj, case_obj, keep_chr_prefix=None,
 
     for variant in vcf_obj:
         formated_variant = build_variant(
-            variant=variant, case_obj=case_obj, case_id=case_id, keep_chr_prefix=keep_chr_prefix
+            variant=variant,
+            case_obj=case_obj,
+            case_id=case_id,
+            genome_build=genome_build,
+            keep_chr_prefix=keep_chr_prefix,
         )
 
         if not formated_variant:

{loqusdb-2.7.19 → loqusdb-2.7.21}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "loqusdb"
-version = "2.7.19"
+version = "2.7.21"
 description = "A simple observation count database"
 authors = ["Your Name <you@example.com>"]
 license = "MIT"

loqusdb-2.7.21/tests/build_models/test_build_variant.py

@@ -0,0 +1,30 @@
+from loqusdb.build_models.variant import get_coords, build_variant
+from loqusdb.constants import GRCH37, GRCH38
+
+
+def test_build_het_variant(het_variant, case_obj):
+    variant_obj = build_variant(variant=het_variant, case_obj=case_obj, genome_build=GRCH37)
+    assert variant_obj["chrom"] == het_variant.CHROM
+    assert variant_obj["homozygote"] == 0
+    assert variant_obj["hemizygote"] == 0
+
+
+def test_get_coords_for_BND(bnd_variant):
+    coords = get_coords(bnd_variant, True, GRCH37)
+    assert coords["pos"] == coords["end"]
+    assert coords["sv_length"] == float("inf")
+    assert coords["sv_type"] == "BND"
+
+
+def test_build_het_variant_grch38(het_variant, case_obj):
+    variant_obj = build_variant(variant=het_variant, case_obj=case_obj, genome_build=GRCH38)
+    assert variant_obj["chrom"] == het_variant.CHROM
+    assert variant_obj["homozygote"] == 0
+    assert variant_obj["hemizygote"] == 0
+
+
+def test_get_coords_for_BND_grch38(bnd_variant):
+    coords = get_coords(bnd_variant, True, GRCH38)
+    assert coords["pos"] == coords["end"]
+    assert coords["sv_length"] == float("inf")
+    assert coords["sv_type"] == "BND"

loqusdb-2.7.21/tests/build_models/test_is_greater.py

@@ -0,0 +1,98 @@
+from loqusdb.build_models.variant import Position, is_greater
+from loqusdb.constants import GRCH37, GRCH38
+
+
+def test_is_greater_different_chrom():
+    ## GIVEN two positions where a is smaller than b. Different chroms
+    a = Position("1", 100)
+    b = Position("3", 100)
+
+    ## WHEN testing if a is greater than b
+    res = is_greater(a, b, genome_build=GRCH37)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+    ## WHEN testing if b is greater than a
+    res = is_greater(b, a, genome_build=GRCH37)
+    ## THEN assert b was greater than a
+    assert res is True
+
+
+def test_is_greater_same_chrom():
+    ## GIVEN two positions where a is smaller than b. Same chroms
+    a = Position("1", 100)
+    b = Position("1", 300)
+
+    ## WHEN testing if a is greater than b
+    res = is_greater(a, b, genome_build=GRCH37)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+    ## WHEN testing if b is greater than a
+    res = is_greater(b, a, genome_build=GRCH37)
+    ## THEN assert b was greater than a
+    assert res is True
+
+
+def test_is_greater_wierd_chrom():
+    ## GIVEN two positions where one chrom is unknown b
+    a = Position("1", 100)
+    b = Position("GRLrs2", 300)
+
+    ## WHEN testing if a is greater than b
+    res = is_greater(a, b, genome_build=GRCH37)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+    ## WHEN testing if b is greater than a
+    res = is_greater(b, a, genome_build=GRCH37)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+
+def test_is_greater_different_chrom_grch38():
+    ## GIVEN two positions where a is smaller than b. Different chroms
+    a = Position("chr1", 100)
+    b = Position("chr3", 100)
+
+    ## WHEN testing if a is greater than b
+    res = is_greater(a, b, genome_build=GRCH38)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+    ## WHEN testing if b is greater than a
+    res = is_greater(b, a, genome_build=GRCH38)
+    ## THEN assert b was greater than a
+    assert res is True
+
+
+def test_is_greater_same_chrom_grch38():
+    ## GIVEN two positions where a is smaller than b. Same chroms
+    a = Position("chr1", 100)
+    b = Position("chr1", 300)
+
+    ## WHEN testing if a is greater than b
+    res = is_greater(a, b, genome_build=GRCH38)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+    ## WHEN testing if b is greater than a
+    res = is_greater(b, a, genome_build=GRCH38)
+    ## THEN assert b was greater than a
+    assert res is True
+
+
+def test_is_greater_wierd_chrom_grch38():
+    ## GIVEN two positions where one chrom is unknown b
+    a = Position("chr1", 100)
+    b = Position("GRLrs2", 300)
+
+    ## WHEN testing if a is greater than b
+    res = is_greater(a, b, genome_build=GRCH38)
+    ## THEN assert a was not greater than b
+    assert res is False
+
+    ## WHEN testing if b is greater than a
+    res = is_greater(b, a, genome_build=GRCH38)
+    ## THEN assert a was not greater than b
+    assert res is False

{loqusdb-2.7.19 → loqusdb-2.7.21}/tests/conftest.py

@@ -332,7 +332,7 @@ def hem_variant(request):
 
 @pytest.fixture(scope="function")
 def variant_chr(request):
-    return CyvcfVariant(chrom="chrX", pos=60000)
+    return CyvcfVariant(chrom="chrX", pos=9000)
 
 
 @pytest.fixture(scope="function")
@@ -437,6 +437,7 @@ def translocation_variant(request):
         info_dict={"END": None, "SVLEN": None, "SVTYPE": "BND"},
     )
 
+
 ##SVs with chr prefix
 @pytest.fixture(scope="function")
 def chr_del_variant(request):

loqusdb-2.7.21/tests/plugins/mongo/test_get_sv.py

@@ -0,0 +1,62 @@
+from loqusdb.build_models.variant import build_variant
+from loqusdb.constants import GRCH37, GRCH38
+
+
+def test_get_insertion(small_insert_variant, mongo_adapter, case_obj):
+    adapter = mongo_adapter
+    ## GIVEN a mongo adapter with a small insertion
+    variant = small_insert_variant
+    case_id = case_obj["case_id"]
+    formated_variant = build_variant(
+        variant=variant, case_obj=case_obj, case_id=case_id, genome_build=GRCH37
+    )
+
+    adapter.add_case(case_obj)
+    adapter.add_structural_variant(formated_variant)
+    for variant_obj in adapter.db.structural_variant.find():
+        assert variant_obj
+
+
+def test_get_translocation(translocation_variant, mongo_adapter, case_obj):
+    adapter = mongo_adapter
+    ## GIVEN a mongo adapter with a translocation
+    variant = translocation_variant
+    case_id = case_obj["case_id"]
+    formated_variant = build_variant(
+        variant=variant, case_obj=case_obj, case_id=case_id, genome_build=GRCH37
+    )
+
+    adapter.add_case(case_obj)
+    adapter.add_structural_variant(formated_variant)
+    for variant_obj in adapter.db.structural_variant.find():
+        assert variant_obj
+
+
+def test_get_insertion_grch38(chr_small_insert_variant, mongo_adapter, case_obj):
+    adapter = mongo_adapter
+    ## GIVEN a mongo adapter with a small insertion
+    variant = chr_small_insert_variant
+    case_id = case_obj["case_id"]
+    formated_variant = build_variant(
+        variant=variant, case_obj=case_obj, case_id=case_id, genome_build=GRCH38
+    )
+
+    adapter.add_case(case_obj)
+    adapter.add_structural_variant(formated_variant)
+    for variant_obj in adapter.db.structural_variant.find():
+        assert variant_obj
+
+
+def test_get_translocation_grch38(chr_translocation_variant, mongo_adapter, case_obj):
+    adapter = mongo_adapter
+    ## GIVEN a mongo adapter with a translocation
+    variant = chr_translocation_variant
+    case_id = case_obj["case_id"]
+    formated_variant = build_variant(
+        variant=variant, case_obj=case_obj, case_id=case_id, genome_build=GRCH38
+    )
+
+    adapter.add_case(case_obj)
+    adapter.add_structural_variant(formated_variant)
+    for variant_obj in adapter.db.structural_variant.find():
+        assert variant_obj