loqusdb 2.7.21__py3-none-any.whl → 2.7.23__py3-none-any.whl

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/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-2.7.21.dist-info → loqusdb-2.7.23.dist-info}/METADATA

@@ -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.dist-info → loqusdb-2.7.23.dist-info}/RECORD

@@ -1,14 +1,14 @@
-loqusdb/__init__.py,sha256=XVjdPPoBf9nwKTdk1RIKAPlBUf5K9iI1qNNMjggiOXU,1415
+loqusdb/__init__.py,sha256=5_jcHx-rbGbtY7B6g-H4Bc9tQwfl440729o0FTAB-RY,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
@@ -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-2.7.21.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
-loqusdb-2.7.21.dist-info/METADATA,sha256=O3-3dPE2wqMdn26vDR9HImJ92dG8sOS2kLhmMKpqBOs,5321
-loqusdb-2.7.21.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-loqusdb-2.7.21.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
-loqusdb-2.7.21.dist-info/RECORD,,
+loqusdb-2.7.23.dist-info/LICENSE,sha256=urpFcJXw3elN9kV2fFutc-lXegjuu2lqP_GSy8_CAbs,1054
+loqusdb-2.7.23.dist-info/METADATA,sha256=U8YWBzq8oZhcjQm_bZWd_6cjRKfYYG7pBHMxERbivAY,5506
+loqusdb-2.7.23.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+loqusdb-2.7.23.dist-info/entry_points.txt,sha256=wFoWzEFjsSgXkj9FMQA8C9ihZoJ9R1XvbGuX9hEEI6E,52
+loqusdb-2.7.23.dist-info/RECORD,,