cool-seq-tool 0.15.0__py3-none-any.whl → 0.15.1__py3-none-any.whl

cool_seq_tool/mappers/liftover.py

@@ -6,7 +6,8 @@ Currently only supports GRCh37 <-> GRCh38
 import logging
 from os import environ
 
-from agct import Converter, Genome
+from agct import Assembly as AgctAssembly
+from agct import Converter
 
 from cool_seq_tool.schemas import Assembly
 from cool_seq_tool.utils import process_chromosome_input
@@ -43,13 +44,13 @@ class LiftOver:
         """
         self.from_37_to_38 = Converter(
             chainfile=chain_file_37_to_38 or LIFTOVER_CHAIN_37_TO_38,
-            from_db=Genome.HG19,
-            to_db=Genome.HG38,
+            from_assembly=AgctAssembly.HG19,
+            to_assembly=AgctAssembly.HG38,
         )
         self.from_38_to_37 = Converter(
             chainfile=chain_file_38_to_37 or LIFTOVER_CHAIN_38_TO_37,
-            from_db=Genome.HG38,
-            to_db=Genome.HG19,
+            from_assembly=AgctAssembly.HG38,
+            to_assembly=AgctAssembly.HG19,
         )
 
     def get_liftover(
@@ -77,9 +78,9 @@ class LiftOver:
         """
         chromosome = process_chromosome_input(chromosome, "LiftOver.get_liftover()")
         if liftover_to_assembly == Assembly.GRCH38:
-            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos)
+            liftover = self.from_37_to_38.convert_coordinate(chromosome, pos, pos)
         elif liftover_to_assembly == Assembly.GRCH37:
-            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos)
+            liftover = self.from_38_to_37.convert_coordinate(chromosome, pos, pos)
         else:
             _logger.warning("%s assembly not supported", liftover_to_assembly)
             liftover = None

cool_seq_tool/resources/status.py

@@ -114,9 +114,9 @@ async def check_status(
             chain_file_38_to_37=chain_file_38_to_37,
         )
     except (FileNotFoundError, ChainfileError):
-        _logger.exception("agct converter setup failed")
+        _logger.exception("`agct` converter setup failed")
     except Exception as e:
-        _logger.critical("Encountered unexpected error setting up agct: %s", e)
+        _logger.critical("Encountered unexpected error setting up `agct`: %s", e)
     else:
         status["liftover"] = True
 

{cool_seq_tool-0.15.0.dist-info → cool_seq_tool-0.15.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cool_seq_tool
-Version: 0.15.0
+Version: 0.15.1
 Summary: Common Operation on Lots of Sequences Tool
 Author: Kori Kuzma, James Stevenson, Katie Stahl, Alex Wagner
 License: MIT License
@@ -46,7 +46,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: asyncpg
 Requires-Dist: boto3
-Requires-Dist: agct>=0.1.0-dev1
+Requires-Dist: agct>=0.2.0rc1
 Requires-Dist: polars~=1.0
 Requires-Dist: biocommons.seqrepo
 Requires-Dist: pydantic<3.0,>=2.0

{cool_seq_tool-0.15.0.dist-info → cool_seq_tool-0.15.1.dist-info}/RECORD

@@ -8,18 +8,18 @@ cool_seq_tool/mappers/__init__.py,sha256=tavpwkNogg_nF1J_kb6Q9jk7ezqdRz063v7BMZ4
 cool_seq_tool/mappers/alignment.py,sha256=kWgYssM8YL-Z13H9GdpL77P7simNcbxltAs9YDXHE54,9640
 cool_seq_tool/mappers/exon_genomic_coords.py,sha256=I59vvswLbXk1fOWLNyNd8NTVT39f5yxTCv20utlTCpo,47361
 cool_seq_tool/mappers/feature_overlap.py,sha256=X5UFClaH6ixRsO2fDLxqjywp-Z0bvNx4uzgBICy394U,9758
-cool_seq_tool/mappers/liftover.py,sha256=lltx9zxfkrb5PHtJlKp3a39JCwPP4e0Zft-mQc1jXL8,3367
+cool_seq_tool/mappers/liftover.py,sha256=vQ2BcSE43ZbY4eCJJqDL6dPPE0UclK7f7NoP2WtEHuA,3459
 cool_seq_tool/mappers/mane_transcript.py,sha256=IluiLBxPQoY-CxkpqpjEBcMlHvrNLa34wdKdQxtKgDY,54613
 cool_seq_tool/resources/__init__.py,sha256=VwUC8YaucTS6SmRirToulZTF6CuvuLQRSxFfSfAovCc,77
 cool_seq_tool/resources/data_files.py,sha256=6d1M5WjeFHdTQpzxqjQ78auQRZvIBVqH8QNCrmRRDXw,4205
-cool_seq_tool/resources/status.py,sha256=iP-4NiSmqV-D--gypZyrSqVbOWQvyBZICKQb-VinTik,6241
+cool_seq_tool/resources/status.py,sha256=W1iINKqHi_YWSbJi1c-vUIVCAnQCzNgO8A34bQcRmz0,6245
 cool_seq_tool/resources/transcript_mapping.tsv,sha256=AO3luYQAbFiCoRgiiPXotakb5pAwx1jDCeXpvGdIuac,24138769
 cool_seq_tool/sources/__init__.py,sha256=51QiymeptF7AeVGgV-tW_9f4pIUr0xtYbyzpvHOCneM,304
 cool_seq_tool/sources/mane_transcript_mappings.py,sha256=PLJymduwvG1pt9mravE58BfJsGXdAYXcZYZdHPy12z0,7211
 cool_seq_tool/sources/transcript_mappings.py,sha256=903RKTMBO2rbKh6iTQ1BEWnY4C7saBFMPw2_4ATuudg,10054
 cool_seq_tool/sources/uta_database.py,sha256=38CQ0QHHh0kA87tdgsJHJiHdJHQc06ylBYfemGFUlZc,36759
-cool_seq_tool-0.15.0.dist-info/licenses/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
-cool_seq_tool-0.15.0.dist-info/METADATA,sha256=MEcG0vc2k8F8lQljcFgkIrabFHJec_pE7Ib6DzLZR2M,6535
-cool_seq_tool-0.15.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-cool_seq_tool-0.15.0.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
-cool_seq_tool-0.15.0.dist-info/RECORD,,
+cool_seq_tool-0.15.1.dist-info/licenses/LICENSE,sha256=IpqC9A-tZW7XXXvCS8c4AVINqkmpxiVA-34Qe3CZSjo,1072
+cool_seq_tool-0.15.1.dist-info/METADATA,sha256=QEHrmJL33DUq1R71GYN5mbBPOdMsCfJImYlvG3TC4U8,6533
+cool_seq_tool-0.15.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+cool_seq_tool-0.15.1.dist-info/top_level.txt,sha256=cGuxdN6p3y16jQf6hCwWhE4OptwUeZPm_PNJlPb3b0k,14
+cool_seq_tool-0.15.1.dist-info/RECORD,,