loqusdb 2.7.20__tar.gz → 2.7.22__tar.gz

{loqusdb-2.7.20 → loqusdb-2.7.22}/PKG-INFO

@@ -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 → loqusdb-2.7.22}/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-2.7.20 → loqusdb-2.7.22}/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-2.7.20 → loqusdb-2.7.22}/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-2.7.20 → loqusdb-2.7.22}/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-2.7.20 → loqusdb-2.7.22}/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 → loqusdb-2.7.22}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "loqusdb"
-version = "2.7.20"
+version = "2.7.22"
 description = "A simple observation count database"
 authors = ["Your Name <you@example.com>"]
 license = "MIT"