loqusdb 2.7.21__tar.gz → 2.7.23__tar.gz

{loqusdb-2.7.21 → loqusdb-2.7.23}/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.3
 Name: loqusdb
-Version: 2.7.21
+Version: 2.7.23
 Summary: A simple observation count database
 License: MIT
-Author: Your Name
-Author-email: you@example.com
+Author: Mans Magnuson
+Author-email: monsunas@gmail.com
+Maintainer: Clinical Genomics Bioinformatics Team
 Requires-Python: >=3.12,<4.0
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
@@ -34,6 +35,8 @@ Right now **Locusdb** uses [mongodb][mongodb] as backend for
 storing variants, but there should not be a huge difference to use another
 database manager.
 
+Find more detailed instructions and examples in the [documentation][docs].
+
 ## Installation ##
 
 
@@ -166,6 +169,7 @@ The collections are defined as follows:
 }
 ```
 
+[docs]: https://clinical-genomics.github.io/loqusdb
 [mongodb]: https://www.mongodb.org
 [publication]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03609-z
 [pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square

{loqusdb-2.7.21 → loqusdb-2.7.23}/README.md

@@ -10,6 +10,8 @@ Right now **Locusdb** uses [mongodb][mongodb] as backend for
 storing variants, but there should not be a huge difference to use another
 database manager.
 
+Find more detailed instructions and examples in the [documentation][docs].
+
 ## Installation ##
 
 
@@ -142,6 +144,7 @@ The collections are defined as follows:
 }
 ```
 
+[docs]: https://clinical-genomics.github.io/loqusdb
 [mongodb]: https://www.mongodb.org
 [publication]: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03609-z
 [pypi-img]: https://img.shields.io/pypi/v/loqusdb.svg?style=flat-square

{loqusdb-2.7.21 → loqusdb-2.7.23}/loqusdb/__init__.py

@@ -4,7 +4,7 @@ from pymongo import ASCENDING, IndexModel
 
 logger = logging.getLogger(__name__)
 
-__version__ = "2.7.21"
+__version__ = "2.7.23"
 
 INDEXES = {
     "variant": [

{loqusdb-2.7.21 → loqusdb-2.7.23}/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-2.7.21 → loqusdb-2.7.23}/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-2.7.21 → loqusdb-2.7.23}/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-2.7.21 → loqusdb-2.7.23}/pyproject.toml

@@ -1,10 +1,14 @@
-[tool.poetry]
+[project]
 name = "loqusdb"
-version = "2.7.21"
+
 description = "A simple observation count database"
-authors = ["Your Name <you@example.com>"]
+authors = [{name="Mans Magnuson", email="monsunas@gmail.com"}, {name="Adam Rosenbaum", email="adam.rosenbaum@regionvasterbotten.se"}, {name="Daniel Nilsson", email="daniel.nilsson@ki.se"}, {name="Chiara Rasi", email="chiara.rasi@scilifelab.se"}, {name="Jesper Eisfeldt", email="jesper.eisfeldt@scilifelab.se"}, {name="Henrik Stranneheim"},]
+maintainers = [ {name="Clinical Genomics Bioinformatics Team"}, {name="Clinical Genomics System Development Team"}, {name="Clinical Genomics Scout Team"}]
 license = "MIT"
 readme = "README.md"
+version = "2.7.23"
+
+[tool.poetry]
 include = [
   "README.md",
   "loqusdb/**/*",
@@ -31,6 +35,11 @@ pre-commit = "*"
 pytest = "*"
 pytest-cov = "*"
 
+[tool.poetry.group.docs.dependencies]
+mkdocs = "*"
+mkdocs-material = "*"
+markdown-include = "*"
+
 [tool.poetry.scripts]
 loqusdb = "loqusdb.commands.cli:cli"