loqusdb 2.7.20__py3-none-any.whl → 2.7.22__py3-none-any.whl

loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.20"
+__version__ = "2.7.22"
 
 INDEXES = {
     "variant": [

loqusdb/build_models/profile_variant.py

@@ -37,7 +37,7 @@ def build_profile_variant(variant, keep_chr_prefix=None):
 
     chrom = variant.CHROM
     if not keep_chr_prefix:
-        if chrom.startswith(("chr", "CHR", "Chr")):
+        if chrom.lower().startswith("chr"):
             chrom = chrom[3:]
 
     pos = int(variant.POS)

loqusdb/build_models/variant.py

@@ -99,7 +99,7 @@ def get_coords(variant, keep_chr_prefix, genome_build):
     }
     chrom = variant.CHROM
     if not keep_chr_prefix:
-        if chrom.startswith(("chr", "CHR", "Chr")):
+        if chrom.lower().startswith("chr"):
             chrom = chrom[3:]
     coordinates["chrom"] = chrom
     end_chrom = chrom
@@ -121,7 +121,7 @@ def get_coords(variant, keep_chr_prefix, genome_build):
         other_coordinates = alt.strip("ATCGN").strip("[]").split(":")
         end_chrom = other_coordinates[0]
         if not keep_chr_prefix:
-            if end_chrom.startswith(("chr", "CHR", "Chr")):
+            if chrom.lower().startswith("chr"):
                 end_chrom = end_chrom[3:]
 
         end = int(other_coordinates[1])

loqusdb/commands/export.py

@@ -56,9 +56,13 @@ def export(ctx, outfile, variant_type, freq):
             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)
+            elif genome == GRCH38:
+                if chrom[3:] in existing_chromosomes:
+                    ordered_chromosomes.append(chrom[3:])
+                    existing_chromosomes.remove(chrom[3:])
+                elif chrom in existing_chromosomes:
+                    ordered_chromosomes.append(chrom)
+                    existing_chromosomes.remove(chrom)
     for chrom in existing_chromosomes:
         ordered_chromosomes.append(chrom)
 

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-2.7.20.dist-info → loqusdb-2.7.22.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.20
+Version: 2.7.22
 Summary: A simple observation count database
 License: MIT
 Author: Your Name

{loqusdb-2.7.20.dist-info → loqusdb-2.7.22.dist-info}/RECORD

@@ -1,21 +1,21 @@
-loqusdb/__init__.py,sha256=HCx0k7_ndzjGnRnnEFruQxC4eQlKosO4gSJ2TP86I1g,1415
+loqusdb/__init__.py,sha256=Y0QmFuaSq7ltbH8xOPBqjJ3cGsEyN4XaFW4giE5d4Ps,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=4_FDSRUGDt-h3lqBJ00kC9QDdTTGzpbEF-s51AjLQLU,8094
+loqusdb/build_models/profile_variant.py,sha256=ORus7IPhMZQyA8C4v822MzXTW4ZXHRSgmTDC7frkfI4,1158
+loqusdb/build_models/variant.py,sha256=QQqCdZCdpeY-l8unc6GVwORBrgjvKpEk85ItD5Toci4,8074
 loqusdb/commands/__init__.py,sha256=BXAN3UADgqPrkGczzjlLO9GyyQ96dnLnP7n92JlYHgo,603
 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/export.py,sha256=mbRPOaUgPerLpH7ZKwyI2IzStAIsywZMHJystasLYec,4271
 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
 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/view.py,sha256=JOpgRnlkWRToD9Y5DfPWJ9x1HvIPFHXpi_dZWt29co4,6582
 loqusdb/commands/wipe.py,sha256=WTOjyNooCUhtmZ6pdcPFa0PZrFc9E_pkLbnat_zP96M,553
 loqusdb/constants/__init__.py,sha256=BpZQYpUF-B9AqoXE2R5XMFuURxH5iNLt1kUJSKMqZGY,2265
 loqusdb/exceptions/__init__.py,sha256=Fq0UQg9TepWh19D7WT3dARyAHvorwJF6phhnZi2AkxE,88
@@ -49,8 +49,8 @@ loqusdb/utils/profiling.py,sha256=uISq4xfRNPPedoYXS_D4dXphq8odDogfMBm_XfHBTpE,92
 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-2.7.20.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,,
+loqusdb-2.7.22.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
+loqusdb-2.7.22.dist-info/METADATA,sha256=UIyXnGX1KUcCWkGadC1Ce3AL17J7EUlKvrVvR3kuKKc,5321
+loqusdb-2.7.22.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+loqusdb-2.7.22.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
+loqusdb-2.7.22.dist-info/RECORD,,