loqusdb 2.7.19__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__ = "2.7.19"
+__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/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/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/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/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/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.dist-info → loqusdb-2.7.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.19
+Version: 2.7.20
 Summary: A simple observation count database
 License: MIT
 Author: Your Name

{loqusdb-2.7.19.dist-info → loqusdb-2.7.20.dist-info}/RECORD

@@ -1,14 +1,14 @@
-loqusdb/__init__.py,sha256=Zs9AtDiQwuASVgXDU0xzuWv8RhaadjMaa9WD4D7BMVc,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=WzWhxq4HNvf67IknyBWYnMHQzPMZ9eitw_so6lfOkPc,1166
-loqusdb/build_models/variant.py,sha256=buIQr8GsNUBBtgf78a0n5I_GiMEogohSEQJibVUuM5Y,7815
+loqusdb/build_models/variant.py,sha256=4_FDSRUGDt-h3lqBJ00kC9QDdTTGzpbEF-s51AjLQLU,8094
 loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,603
 loqusdb/commands/annotate.py,sha256=MGU9EerKYsFx1lkyjQ6ZMUKYuShi0uSTPJCS0cyxq7U,1467
-loqusdb/commands/cli.py,sha256=XRprLQaENiLdqXG_7ugCC9jTcG7Uh54_M0KZj1ERFaM,3542
+loqusdb/commands/cli.py,sha256=lRgOYN3JDE81z3EUdqc5-eU7i0m5XF8p0WZvI3svQ3g,3577
 loqusdb/commands/delete.py,sha256=BRtm6Uade3l97FBcKFNkiYjks84AhuXYo-2QD8E74A4,2120
-loqusdb/commands/export.py,sha256=HKoRzUo_BHNOdw_TcKUId9TTowi8VJVGqnuDlK-FqFE,3531
+loqusdb/commands/export.py,sha256=3eV0pYfkD73qoB0_Y2_wpxV0xOrCAppVoPs9C815zyI,4078
 loqusdb/commands/identity.py,sha256=KLA9c8e6cJFDxtqIa1G6zdHTHK1sz2b3v1Utdtik_4k,787
 loqusdb/commands/load.py,sha256=pHtjldblUM-HFFgcN5UtoaxGhYmo1yeexqGq4I427qk,4996
 loqusdb/commands/load_profile.py,sha256=x-T2bzi2SL5kwZhY_3hHQCtGDLao1xkxj1pZaOnzs4U,3436
@@ -17,7 +17,7 @@ loqusdb/commands/restore.py,sha256=eqPX0yao0IAYS5SbjCdlsfSJRBbRByBLISUU2hTzqqs,1
 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
@@ -42,15 +42,15 @@ loqusdb/resources/maf_50_sites_GRCh38.vcf.gz,sha256=6T4iyrIr6yx1HpgobzAsh305BO1J
 loqusdb/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 loqusdb/utils/annotate.py,sha256=vOHlLkenwCCLXh-cjerd9cW68eZfEtgvP0IwWh-oBHs,2347
 loqusdb/utils/case.py,sha256=aeTvyACJTDjzl-aOjAZaUzFMLisgFKMfcoXSvNAZz4s,2168
-loqusdb/utils/delete.py,sha256=uj1m5i12GjUhhnCnIbh6D7BMG-oMDk6bfrJxk8zpSxE,5208
+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=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=og8JBYock31v_0CnsoRhuKIJCurLCIFW8PCCQIRWF-Q,5207
-loqusdb-2.7.19.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.19.dist-info/METADATA,sha256=w1TxeA5Lz1cYqetHRw0UGvuEUS82WfpOgxThm5hQOYs,5321
-loqusdb-2.7.19.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-loqusdb-2.7.19.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
-loqusdb-2.7.19.dist-info/RECORD,,
+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,,