loqusdb 2.7.18__py3-none-any.whl → 2.7.20__py3-none-any.whl

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/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/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/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/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/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/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/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/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/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/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/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:

loqusdb/utils/load.py

@@ -32,6 +32,7 @@ def load_database(
     skip_case_id=False,
     gq_threshold=None,
     snv_gq_only=False,
+    keep_chr_prefix=False,
     qual_gq=False,
     case_id=None,
     max_window=3000,
@@ -51,6 +52,7 @@ def load_database(
           family_type(str): Format of family file
           skip_case_id(bool): If no case information should be added to variants
           gq_threshold(int): If only quality variants should be considered
+          keep_chr_prefix(bool): Retain chr/CHR/Chr prefix when present
           qual_gq(bool): Use QUAL field instead of GQ format tag to gate quality
           case_id(str): If different case id than the one in family file should be used
           max_window(int): Specify the max size for sv windows
@@ -68,7 +70,7 @@ def load_database(
     nr_variants = None
     vcf_individuals = None
     if variant_file:
-        vcf_info = check_vcf(variant_file)
+        vcf_info = check_vcf(variant_file, keep_chr_prefix)
         nr_variants = vcf_info["nr_variants"]
         variant_type = vcf_info["variant_type"]
         vcf_files.append(variant_file)
@@ -78,7 +80,7 @@ def load_database(
     nr_sv_variants = None
     sv_individuals = None
     if sv_file:
-        vcf_info = check_vcf(sv_file, "sv")
+        vcf_info = check_vcf(sv_file, keep_chr_prefix, "sv")
         nr_sv_variants = vcf_info["nr_variants"]
         vcf_files.append(sv_file)
         sv_individuals = vcf_info["individuals"]
@@ -86,7 +88,7 @@ def load_database(
     profiles = None
     matches = None
     if profile_file:
-        profiles = get_profiles(adapter, profile_file)
+        profiles = get_profiles(adapter, profile_file, keep_chr_prefix)
         ###Check if any profile already exists
         matches = profile_match(
             adapter, profiles, hard_threshold=hard_threshold, soft_threshold=soft_threshold
@@ -152,6 +154,7 @@ def load_database(
                 skip_case_id=skip_case_id,
                 gq_threshold=gq_threshold if not snv_gq_only or variant_type == "snv" else None,
                 qual_gq=qual_gq,
+                keep_chr_prefix=keep_chr_prefix,
                 max_window=max_window,
                 variant_type=variant_type,
                 genome_build=genome_build,
@@ -200,6 +203,7 @@ def load_variants(
     skip_case_id=False,
     gq_threshold=None,
     qual_gq=False,
+    keep_chr_prefix=False,
     max_window=3000,
     variant_type="snv",
     genome_build=None,
@@ -213,6 +217,7 @@ def load_variants(
         case_obj(Case): dict with case information
         skip_case_id (bool): whether to include the case id on variant level
                              or not
+        keep_chr_prefix(bool): Retain chr/CHR/Chr prefix when present
         gq_threshold(int)
         qual_gq(bool): whether to use QUAL instead of GQ
         max_window(int): Specify the max size for sv windows
@@ -242,6 +247,7 @@ def load_variants(
                 case_id,
                 gq_threshold,
                 qual_gq,
+                keep_chr_prefix,
                 ignore_gq_if_unset,
                 genome_build=genome_build,
             )
@@ -263,7 +269,7 @@ def load_variants(
     return nr_inserted
 
 
-def load_profile_variants(adapter, variant_file):
+def load_profile_variants(adapter, variant_file, keep_chr_prefix=None):
     """
 
     Loads variants used for profiling
@@ -275,7 +281,7 @@ def load_profile_variants(adapter, variant_file):
 
     """
 
-    vcf_info = check_vcf(variant_file)
+    vcf_info = check_vcf(variant_file, keep_chr_prefix)
     variant_type = vcf_info["variant_type"]
 
     if variant_type != "snv":
@@ -284,5 +290,5 @@ def load_profile_variants(adapter, variant_file):
 
     vcf = get_vcf(variant_file)
 
-    profile_variants = [build_profile_variant(variant) for variant in vcf]
+    profile_variants = [build_profile_variant(variant, keep_chr_prefix) for variant in vcf]
     adapter.add_profile_variants(profile_variants)

loqusdb/utils/profiling.py

@@ -11,7 +11,7 @@ from .vcf import get_file_handle
 LOG = logging.getLogger(__name__)
 
 
-def get_profiles(adapter, vcf_file):
+def get_profiles(adapter, vcf_file, keep_chr_prefix):
     """Given a vcf, get a profile string for each sample in the vcf
     based on the profile variants in the database
 
@@ -44,7 +44,7 @@ def get_profiles(adapter, vcf_file):
         found_variant = False
         for variant in vcf(region):
 
-            variant_id = get_variant_id(variant)
+            variant_id = get_variant_id(variant, keep_chr_prefix)
 
             # If variant id i.e. chrom_pos_ref_alt matches
             if variant_id == profile_variant["_id"]:
@@ -183,7 +183,7 @@ def compare_profiles(profile1, profile2):
     return similarity_ratio
 
 
-def update_profiles(adapter):
+def update_profiles(adapter, keep_chr_prefix):
     """
     For all cases having vcf_path, update the profile string for the samples
 
@@ -198,7 +198,7 @@ def update_profiles(adapter):
         # case with new profiled individuals.
         if case.get("profile_path"):
 
-            profiles = get_profiles(adapter, case["profile_path"])
+            profiles = get_profiles(adapter, case["profile_path"], keep_chr_prefix)
             profiled_individuals = deepcopy(case["individuals"])
 
             for individual in profiled_individuals:

loqusdb/utils/vcf.py

@@ -89,7 +89,7 @@ def check_sorting(previous_chrom, previous_pos, current_chrom, current_pos):
     pass
 
 
-def check_vcf(vcf_path, expected_type="snv"):
+def check_vcf(vcf_path, keep_chr_prefix=None, expected_type="snv"):
     """Check if there are any problems with the vcf file
 
     Args:
@@ -113,7 +113,7 @@ def check_vcf(vcf_path, expected_type="snv"):
     previous_pos = None
     previous_chrom = None
 
-    posititon_variants = set()
+    position_variants = set()
 
     nr_variants = 0
     for nr_variants, variant in enumerate(vcf, 1):
@@ -134,36 +134,36 @@ def check_vcf(vcf_path, expected_type="snv"):
         variant_id = "{0}_{1}".format(current_chrom, current_pos)
         # For SNVs we can create a proper variant id with chrom_pos_ref_alt
         if variant_type == "snv":
-            variant_id = get_variant_id(variant)
+            variant_id = get_variant_id(variant, keep_chr_prefix)
 
         # Initiate variables
         if not previous_chrom:
             previous_chrom = current_chrom
             previous_pos = current_pos
-            posititon_variants = {variant_id}
+            position_variants = {variant_id}
             continue
 
         # Update variables if new chromosome
         if current_chrom != previous_chrom:
             previous_chrom = current_chrom
             previous_pos = current_pos
-            posititon_variants = {variant_id}
+            position_variants = {variant_id}
             continue
 
         if variant_type == "snv":
             # Check if variant is unique
             if current_pos == previous_pos:
-                if variant_id in posititon_variants:
+                if variant_id in position_variants:
                     raise VcfError("Variant {0} occurs several times" " in vcf".format(variant_id))
                 else:
-                    posititon_variants.add(variant_id)
+                    position_variants.add(variant_id)
             # Check if vcf is sorted
             else:
                 if not current_pos >= previous_pos:
                     raise VcfError("Vcf if not sorted in a correct way")
                 previous_pos = current_pos
-                # Reset posititon_variants since we are on a new position
-                posititon_variants = {variant_id}
+                # Reset position_variants since we are on a new position
+                position_variants = {variant_id}
 
     if variant_type != expected_type:
         raise VcfError(

{loqusdb-2.7.18.dist-info → loqusdb-2.7.20.dist-info}/METADATA

@@ -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.dist-info → loqusdb-2.7.20.dist-info}/RECORD

@@ -1,23 +1,23 @@
-loqusdb/__init__.py,sha256=r4jbFPCtsyXv8VehXkXxBx1HDPPeaidp1mmwpN_Ghrg,1688
+loqusdb/__init__.py,sha256=HCx0k7_ndzjGnRnnEFruQxC4eQlKosO4gSJ2TP86I1g,1415
 loqusdb/__main__.py,sha256=8FGKySAGaWSzAYMj6HRsxeyiME3V01Idt7HrmN7pSYY,397
 loqusdb/build_models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/build_models/case.py,sha256=AByutEYK2N3kS9JFvyZfPKNZdCpZHCSD0nNHAgaU1Cs,4127
-loqusdb/build_models/profile_variant.py,sha256=TbSxfVjESstS_FgbkOW4NQwMQVeTyhn9oc9yPZmDhzI,1021
-loqusdb/build_models/variant.py,sha256=Vee9FVwCC03wo6u2uI7qH9rgfevndBf364YSmE3Js2k,7271
+loqusdb/build_models/profile_variant.py,sha256=WzWhxq4HNvf67IknyBWYnMHQzPMZ9eitw_so6lfOkPc,1166
+loqusdb/build_models/variant.py,sha256=4_FDSRUGDt-h3lqBJ00kC9QDdTTGzpbEF-s51AjLQLU,8094
 loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,603
-loqusdb/commands/annotate.py,sha256=748kImopE5WbaO1nuv3WUgIqezWFSsi7SBeWhOz26-s,1384
-loqusdb/commands/cli.py,sha256=wJD5S1BoCxtRTAobd1QtmQpzlngJg-mt1nsyD92fDD4,3176
-loqusdb/commands/delete.py,sha256=R6ysHKSMw1mmL4ZbktoUIKzdzDLQ3314YPYhIy1myic,1979
-loqusdb/commands/export.py,sha256=HKoRzUo_BHNOdw_TcKUId9TTowi8VJVGqnuDlK-FqFE,3531
+loqusdb/commands/annotate.py,sha256=MGU9EerKYsFx1lkyjQ6ZMUKYuShi0uSTPJCS0cyxq7U,1467
+loqusdb/commands/cli.py,sha256=lRgOYN3JDE81z3EUdqc5-eU7i0m5XF8p0WZvI3svQ3g,3577
+loqusdb/commands/delete.py,sha256=BRtm6Uade3l97FBcKFNkiYjks84AhuXYo-2QD8E74A4,2120
+loqusdb/commands/export.py,sha256=3eV0pYfkD73qoB0_Y2_wpxV0xOrCAppVoPs9C815zyI,4078
 loqusdb/commands/identity.py,sha256=KLA9c8e6cJFDxtqIa1G6zdHTHK1sz2b3v1Utdtik_4k,787
-loqusdb/commands/load.py,sha256=QMUSzdaCi1lVC9F4u0xkAJtVz4N_tMPh3Nu6Obl9ky4,4903
-loqusdb/commands/load_profile.py,sha256=cflCbF9f77_HCH8xPnN8zSSocvIffRMnC2LPE0j7Xq8,3336
+loqusdb/commands/load.py,sha256=pHtjldblUM-HFFgcN5UtoaxGhYmo1yeexqGq4I427qk,4996
+loqusdb/commands/load_profile.py,sha256=x-T2bzi2SL5kwZhY_3hHQCtGDLao1xkxj1pZaOnzs4U,3436
 loqusdb/commands/migrate.py,sha256=2C8YL-zVqnpnqg3JIyUr0rbVnb8-AGPVWNhicHnPKLo,667
 loqusdb/commands/restore.py,sha256=eqPX0yao0IAYS5SbjCdlsfSJRBbRByBLISUU2hTzqqs,1492
 loqusdb/commands/update.py,sha256=zz3wueaJVqJ1FKact-rpY2az__5oa1LnZKf7mgqNGPk,3211
 loqusdb/commands/view.py,sha256=PkwyvzQgq5ArrEakI-lKQThrhjBLLl2gYejHI2g13WU,5197
 loqusdb/commands/wipe.py,sha256=WTOjyNooCUhtmZ6pdcPFa0PZrFc9E_pkLbnat_zP96M,553
-loqusdb/constants/__init__.py,sha256=r6y2TN8BqbKuh2Uyxq0trh-3A9xiWeStqWlvEPp-rSA,1645
+loqusdb/constants/__init__.py,sha256=BpZQYpUF-B9AqoXE2R5XMFuURxH5iNLt1kUJSKMqZGY,2265
 loqusdb/exceptions/__init__.py,sha256=Fq0UQg9TepWh19D7WT3dARyAHvorwJF6phhnZi2AkxE,88
 loqusdb/exceptions/case.py,sha256=n3mGF7RIc1imQFxnNJ1TWxeJeMWN4MHsKxoZb0m1-Os,92
 loqusdb/exceptions/profile.py,sha256=TVkRXh3ZbkNCmFHzZTCuhPP3iFWBwP1YQGD8IlSoCTo,98
@@ -40,17 +40,17 @@ loqusdb/resources/loqusdb.20181005.gz,sha256=DI8CLI7fPnIAjM25Avraz-C7KQkOKsfnhgZ
 loqusdb/resources/maf_50_sites_GRCh37.vcf.gz,sha256=BoD1_xZ-Rr8DTWCMNlQGh7gz1K8FA-j2nC4jKn_eB2A,5260
 loqusdb/resources/maf_50_sites_GRCh38.vcf.gz,sha256=6T4iyrIr6yx1HpgobzAsh305BO1JX0oGj48nFiYt2QM,9037
 loqusdb/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-loqusdb/utils/annotate.py,sha256=cPNWlhsv6yoe3lxNfa9DytO5eACuM_mOJJw_mglVMN0,2646
+loqusdb/utils/annotate.py,sha256=vOHlLkenwCCLXh-cjerd9cW68eZfEtgvP0IwWh-oBHs,2347
 loqusdb/utils/case.py,sha256=aeTvyACJTDjzl-aOjAZaUzFMLisgFKMfcoXSvNAZz4s,2168
-loqusdb/utils/delete.py,sha256=-ddBM_QXKzlUN6egEJggKzXX1P-WEdi92HgaD1DJRtg,4843
-loqusdb/utils/load.py,sha256=LyYHPwaCVV-7edbaoPahah05yPfG9H4VCYSg1gmz_M0,9063
+loqusdb/utils/delete.py,sha256=X2SA0IdynoLcV-LwSg_Y_jqh-1uDRE6EoaVTiCWSPPM,5582
+loqusdb/utils/load.py,sha256=GgJyTLSOpgcEqjvo9RXzcacQLzHZYtXF_tkyp_XJwOs,9448
 loqusdb/utils/migrate.py,sha256=9Q6kdIi9TpFVzDYptlEE8RqPPS5wyzfM3F8egzmmBBk,1113
-loqusdb/utils/profiling.py,sha256=3OizF7CpYvSl9kyl2g4KGJxbIRUqWfmfLxn3843XYDk,9164
+loqusdb/utils/profiling.py,sha256=uISq4xfRNPPedoYXS_D4dXphq8odDogfMBm_XfHBTpE,9232
 loqusdb/utils/update.py,sha256=1edJG-u24FgOSxyXAQEiyTG4IyK-Uo3lSIl5qyzcXsI,4433
 loqusdb/utils/variant.py,sha256=U6nMZRUf5NDDQ74nG0HBCLMnFQVgFAT6eHll_F2uiwc,2087
-loqusdb/utils/vcf.py,sha256=ybmrTBEPYa0FbUXo8ttlwATk13RnKjX9eIDbRDwCiVE,5175
-loqusdb-2.7.18.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.18.dist-info/METADATA,sha256=yTsm5y8i4u_chGfnAbMm5ZfjorJOVZQfl4qK9vdJDCk,5321
-loqusdb-2.7.18.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-loqusdb-2.7.18.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
-loqusdb-2.7.18.dist-info/RECORD,,
+loqusdb/utils/vcf.py,sha256=og8JBYock31v_0CnsoRhuKIJCurLCIFW8PCCQIRWF-Q,5207
+loqusdb-2.7.20.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
+loqusdb-2.7.20.dist-info/METADATA,sha256=efArcCfHQNeSsFf5C2EPYII5cYFYTf80nmIIpLLFanM,5321
+loqusdb-2.7.20.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+loqusdb-2.7.20.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
+loqusdb-2.7.20.dist-info/RECORD,,