loqusdb 2.7.18__tar.gz → 2.7.20__tar.gz

{loqusdb-2.7.18 → loqusdb-2.7.20}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.18
+Version: 2.7.20
 Summary: A simple observation count database
 License: MIT
 Author: Your Name

{loqusdb-2.7.18 → loqusdb-2.7.20}/loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.18"
+__version__ = "2.7.20"
 
 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-2.7.18 → loqusdb-2.7.20}/loqusdb/build_models/profile_variant.py

@@ -24,23 +24,25 @@ def get_maf(variant):
     return variant.INFO.get("MAF")
 
 
-def build_profile_variant(variant):
+def build_profile_variant(variant, keep_chr_prefix=None):
     """Returns a ProfileVariant object
 
     Args:
         variant (cyvcf2.Variant)
+        keep_chr_prefix(bool): Retain chr/CHR/Chr prefix when present
 
     Returns:
         variant (models.ProfileVariant)
     """
 
     chrom = variant.CHROM
-    if chrom.startswith(("chr", "CHR", "Chr")):
-        chrom = chrom[3:]
+    if not keep_chr_prefix:
+        if chrom.startswith(("chr", "CHR", "Chr")):
+            chrom = chrom[3:]
 
     pos = int(variant.POS)
 
-    variant_id = get_variant_id(variant)
+    variant_id = get_variant_id(variant, keep_chr_prefix)
 
     ref = variant.REF
     alt = variant.ALT[0]

{loqusdb-2.7.18 → loqusdb-2.7.20}/loqusdb/build_models/variant.py

@@ -15,49 +15,59 @@ 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, [])
     )
 
 
-def get_variant_id(variant):
-    """Get a variant id on the format chrom_pos_ref_alt"""
+def get_variant_id(variant, keep_chr_prefix=None):
+    """Get a variant id on the format chrom_pos_ref_alt
+
+    Args:
+        variant (cyvcf2.Variant)
+        keep_chr_prefix(bool): Retain chr/CHR/Chr prefix when present
+
+    Returns:
+        variant (models.ProfileVariant)
+    """
+
     chrom = variant.CHROM
-    if chrom.lower().startswith("chr"):
-        chrom = chrom[3:]
+    if not keep_chr_prefix:
+        if chrom.lower().startswith("chr"):
+            chrom = chrom[3:]
     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
@@ -68,11 +78,13 @@ def is_greater(a, b):
     return a_chrom == b_chrom and a.pos > b.pos
 
 
-def get_coords(variant):
+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)
@@ -86,8 +98,9 @@ def get_coords(variant):
         "end": None,
     }
     chrom = variant.CHROM
-    if chrom.startswith(("chr", "CHR", "Chr")):
-        chrom = chrom[3:]
+    if not keep_chr_prefix:
+        if chrom.startswith(("chr", "CHR", "Chr")):
+            chrom = chrom[3:]
     coordinates["chrom"] = chrom
     end_chrom = chrom
 
@@ -107,8 +120,9 @@ def get_coords(variant):
     if sv_type == "BND":
         other_coordinates = alt.strip("ATCGN").strip("[]").split(":")
         end_chrom = other_coordinates[0]
-        if end_chrom.startswith(("chr", "CHR", "Chr")):
-            end_chrom = end_chrom[3:]
+        if not keep_chr_prefix:
+            if end_chrom.startswith(("chr", "CHR", "Chr")):
+                end_chrom = end_chrom[3:]
 
         end = int(other_coordinates[1])
 
@@ -126,7 +140,7 @@ def get_coords(variant):
     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
 
@@ -148,6 +162,7 @@ def build_variant(
     case_id: Optional[str] = None,
     gq_threshold: Optional[int] = None,
     gq_qual: Optional[bool] = False,
+    keep_chr_prefix: Optional[bool] = False,
     ignore_gq_if_unset: Optional[bool] = False,
     genome_build: Optional[str] = None,
 ) -> Variant:
@@ -165,6 +180,7 @@ def build_variant(
         case_id(str): The case id
         gq_threshold(int): Genotype Quality threshold
         gq_qual(bool): Use variant.QUAL for quality instead of GQ
+        keep_chr_prefix(bool): Retain chr/CHR/Chr prefix when present
         ignore_gq_if_unset(bool): Ignore GQ threshold check for variants that do not have GQ or QUAL set.
         genome_build(str): Genome build. Ex. GRCh37 or GRCh38
 
@@ -179,14 +195,14 @@ def build_variant(
         sv = True
 
     # chrom_pos_ref_alt
-    variant_id = get_variant_id(variant)
+    variant_id = get_variant_id(variant, keep_chr_prefix)
 
     ref = variant.REF
     # ALT is an array in cyvcf2
     # We allways assume splitted and normalized VCFs
     alt = variant.ALT[0]
 
-    coordinates = get_coords(variant)
+    coordinates = get_coords(variant, keep_chr_prefix, genome_build=genome_build)
     chrom = coordinates["chrom"]
     pos = coordinates["pos"]
 
@@ -224,7 +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-2.7.18 → loqusdb-2.7.20}/loqusdb/commands/annotate.py

@@ -21,6 +21,7 @@ LOG = logging.getLogger(__name__)
 def annotate(ctx, variant_file, sv):
     """Annotate the variants in a VCF"""
     adapter = ctx.obj["adapter"]
+    keep_chr_prefix = ctx.obj["keep_chr_prefix"]
 
     variant_path = os.path.abspath(variant_file)
 
@@ -40,9 +41,9 @@ def annotate(ctx, variant_file, sv):
     start_inserting = datetime.now()
 
     if sv:
-        annotated_variants = annotate_svs(adapter, vcf_obj)
+        annotated_variants = annotate_svs(adapter, vcf_obj, keep_chr_prefix)
     else:
-        annotated_variants = annotate_snvs(adapter, vcf_obj)
+        annotated_variants = annotate_snvs(adapter, vcf_obj, keep_chr_prefix)
     # try:
     for variant in annotated_variants:
         click.echo(str(variant).rstrip())

{loqusdb-2.7.18 → loqusdb-2.7.20}/loqusdb/commands/cli.py

@@ -52,14 +52,35 @@ 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",
 )
+@click.option(
+    "--keep-chr-prefix",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Retain the 'chr/Chr/CHR' prefix for chromosomes if it is present",
+)
 @click.option("-v", "--verbose", is_flag=True)
 @click.version_option(__version__)
 @click.pass_context
 def cli(
-    ctx, database, username, password, authdb, port, host, uri, verbose, config, test, genome_build
+    ctx,
+    database,
+    username,
+    password,
+    authdb,
+    port,
+    host,
+    uri,
+    verbose,
+    config,
+    test,
+    genome_build,
+    keep_chr_prefix,
 ):
     """loqusdb: manage a local variant count database."""
     loglevel = "INFO"
@@ -102,7 +123,8 @@ 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 = {}
     ctx.obj["db"] = database
@@ -114,3 +136,4 @@ def cli(
     ctx.obj["adapter"] = adapter
     ctx.obj["version"] = __version__
     ctx.obj["genome_build"] = genome_build
+    ctx.obj["keep_chr_prefix"] = keep_chr_prefix

{loqusdb-2.7.18 → loqusdb-2.7.20}/loqusdb/commands/delete.py

@@ -35,6 +35,7 @@ def delete(ctx, family_file, family_type, case_id):
         ctx.abort()
 
     adapter = ctx.obj["adapter"]
+    keep_chr_prefix = ctx.obj["keep_chr_prefix"]
 
     # Get a ped_parser.Family object from family file
     family = None
@@ -59,7 +60,12 @@ def delete(ctx, family_file, family_type, case_id):
     genome_build = ctx.obj["genome_build"]
     start_deleting = datetime.now()
     try:
-        delete_command(adapter=adapter, case_obj=existing_case, genome_build=genome_build)
+        delete_command(
+            adapter=adapter,
+            case_obj=existing_case,
+            genome_build=genome_build,
+            keep_chr_prefix=keep_chr_prefix,
+        )
     except (CaseError, IOError) as error:
         LOG.warning(error)
         ctx.abort()

{loqusdb-2.7.18 → loqusdb-2.7.20}/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-2.7.18 → loqusdb-2.7.20}/loqusdb/commands/load.py

@@ -148,7 +148,7 @@ def load(
 
     adapter = ctx.obj["adapter"]
     genome_build = ctx.obj["genome_build"]
-
+    keep_chr_prefix = ctx.obj["keep_chr_prefix"]
     start_inserting = datetime.now()
 
     try:
@@ -162,6 +162,7 @@ def load(
             case_id=case_id,
             gq_threshold=gq_threshold,
             snv_gq_only=snv_gq_only,
+            keep_chr_prefix=keep_chr_prefix,
             qual_gq=qual_gq,
             max_window=max_window,
             profile_file=variant_profile_path,

{loqusdb-2.7.18 → loqusdb-2.7.20}/loqusdb/commands/load_profile.py

@@ -60,13 +60,14 @@ def load_profile(ctx, load, variant_file, update, stats, profile_threshold, chec
     """
 
     adapter = ctx.obj["adapter"]
+    keep_chr_prefix = ctx.obj["keep_chr_prefix"]
 
     LOG.info("Running loqusdb profile")
 
     if check_vcf:
         LOG.info(f"Check if profile in {check_vcf} has match in database")
         vcf_file = check_vcf
-        profiles = get_profiles(adapter, vcf_file)
+        profiles = get_profiles(adapter, vcf_file, keep_chr_prefix)
         duplicate = check_duplicates(adapter, profiles, profile_threshold)
 
         if duplicate is not None:
@@ -81,11 +82,11 @@ def load_profile(ctx, load, variant_file, update, stats, profile_threshold, chec
         if variant_file is not None:
             vcf_path = variant_file
         LOG.info(f"Loads variants in {vcf_path} to be used in profiling")
-        load_profile_variants(adapter, vcf_path)
+        load_profile_variants(adapter, vcf_path, keep_chr_prefix)
 
     if update:
         LOG.info("Updates profiles in database")
-        update_profiles(adapter)
+        update_profiles(adapter, keep_chr_prefix)
 
     if stats:
         LOG.info("Prints profile stats")

{loqusdb-2.7.18 → loqusdb-2.7.20}/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-2.7.18 → loqusdb-2.7.20}/loqusdb/utils/annotate.py

@@ -31,21 +31,7 @@ def annotate_variant(variant, var_obj=None):
     return variant
 
 
-def annotate_snv(adpter, variant):
-    """Annotate an SNV/INDEL variant
-
-    Args:
-        adapter(loqusdb.plugin.adapter)
-        variant(cyvcf2.Variant)
-    """
-    variant_id = get_variant_id(variant)
-    variant_obj = adapter.get_variant(variant={"_id": variant_id})
-
-    annotated_variant = annotated_variant(variant, variant_obj)
-    return annotated_variant
-
-
-def annotate_svs(adapter, vcf_obj):
+def annotate_svs(adapter, vcf_obj, keep_chr_prefix):
     """Annotate all SV variants in a VCF
 
     Args:
@@ -56,14 +42,14 @@ def annotate_svs(adapter, vcf_obj):
         variant(cyvcf2.Variant)
     """
     for nr_variants, variant in enumerate(vcf_obj, 1):
-        variant_info = get_coords(variant)
+        variant_info = get_coords(variant, keep_chr_prefix)
         match = adapter.get_structural_variant(variant_info)
         if match:
             annotate_variant(variant, match)
         yield variant
 
 
-def annotate_snvs(adapter, vcf_obj):
+def annotate_snvs(adapter, vcf_obj, keep_chr_prefix):
     """Annotate all variants in a VCF
 
     Args:
@@ -77,7 +63,7 @@ def annotate_snvs(adapter, vcf_obj):
 
     for nr_variants, variant in enumerate(vcf_obj, 1):
         # Add the variant to current batch
-        variants[get_variant_id(variant)] = variant
+        variants[get_variant_id(variant, keep_chr_prefix)] = variant
         # If batch len == 1000 we annotate the batch
         if (nr_variants % 1000) == 0:
 

{loqusdb-2.7.18 → loqusdb-2.7.20}/loqusdb/utils/delete.py

@@ -9,7 +9,9 @@ from loqusdb.build_models.variant import build_variant
 LOG = logging.getLogger(__name__)
 
 
-def delete(adapter, case_obj, update=False, existing_case=False, genome_build=None):
+def delete(
+    adapter, case_obj, keep_chr_prefix=None, update=False, existing_case=False, genome_build=None
+):
     """Delete a case and all of it's variants from the database.
 
     Args:
@@ -18,6 +20,8 @@ def delete(adapter, case_obj, update=False, existing_case=False, genome_build=No
         update(bool): If we are in the middle of an update
         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
@@ -36,7 +40,11 @@ def delete(adapter, case_obj, update=False, existing_case=False, genome_build=No
         if file_type == "vcf_path":
             LOG.info("deleting variants")
             delete_variants(
-                adapter=adapter, vcf_obj=vcf_obj, case_obj=case_obj, genome_build=genome_build
+                adapter=adapter,
+                vcf_obj=vcf_obj,
+                keep_chr_prefix=keep_chr_prefix,
+                case_obj=case_obj,
+                genome_build=genome_build,
             )
         elif file_type == "vcf_sv_path":
             LOG.info("deleting structural variants")
@@ -44,10 +52,14 @@ def delete(adapter, case_obj, update=False, existing_case=False, genome_build=No
                 adapter=adapter,
                 vcf_obj=vcf_obj,
                 case_obj=case_obj,
+                keep_chr_prefix=keep_chr_prefix,
+                genome_build=genome_build,
             )
 
 
-def delete_variants(adapter, vcf_obj, case_obj, case_id=None, genome_build=None):
+def delete_variants(
+    adapter, vcf_obj, case_obj, keep_chr_prefix=None, case_id=None, genome_build=None
+):
     """Delete variants for a case in the database
 
     Args:
@@ -55,6 +67,7 @@ def delete_variants(adapter, vcf_obj, case_obj, case_id=None, genome_build=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
@@ -69,7 +82,11 @@ def delete_variants(adapter, vcf_obj, case_obj, case_id=None, genome_build=None)
     variant_list = []
     for variant in vcf_obj:
         formated_variant = build_variant(
-            variant=variant, case_obj=case_obj, case_id=case_id, genome_build=genome_build
+            variant=variant,
+            case_obj=case_obj,
+            keep_chr_prefix=keep_chr_prefix,
+            case_id=case_id,
+            genome_build=genome_build,
         )
 
         if not formated_variant:
@@ -109,7 +126,9 @@ def delete_variants(adapter, vcf_obj, case_obj, case_id=None, genome_build=None)
     return nr_deleted
 
 
-def delete_structural_variants(adapter, vcf_obj, case_obj, 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:
@@ -117,6 +136,7 @@ def delete_structural_variants(adapter, vcf_obj, case_obj, case_id=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"""
@@ -133,6 +153,8 @@ def delete_structural_variants(adapter, vcf_obj, case_obj, case_id=None):
             variant=variant,
             case_obj=case_obj,
             case_id=case_id,
+            genome_build=genome_build,
+            keep_chr_prefix=keep_chr_prefix,
         )
 
         if not formated_variant: