Add SNP.info property and call it from Tree.query_snp_path (#28)

Author: dpoznik

CHANGELOG.md

@@ -7,7 +7,15 @@ Format based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 
 No unreleased changes
 
-[Unreleased]: https://github.com/23andMe/yhaplo/compare/2.1.6..HEAD
+[Unreleased]: https://github.com/23andMe/yhaplo/compare/2.1.7..HEAD
+
+
+## [2.1.7] - 2024-02-23
+
+### Added
+- `SNP.info` property, called from `Tree.query_snp_path`
+
+[2.1.7]: https://github.com/23andMe/yhaplo/compare/2.1.6..2.1.7
 
 
 ## [2.1.6] - 2024-02-07
@@ -73,7 +81,7 @@ and faster processing of most input types.
 - BCF support
 - Automated tests
 - Optional dependencies
-- `Sample` subclasses: `TextSample`, `VCFSample`, `AblockSample`
+- `Sample` subclasses: `TextSample`, `VCFSample`
 - `CHANGELOG.md`
 
 ### Changed

yhaplo/api/command_line_args.py

@@ -92,8 +92,8 @@ def get_command_line_args(set_defaults: bool = False) -> argparse.Namespace:
         action="store_true",
         help="Generate all auxiliary output.\n"
         "Equivalent to these seven options:\n"
-        "--ancDerCounts --haplogroupPaths --haplogroupPathsDetail\n"
-        "--derSNPs --derSNPsDetail --ancSNPs --ancSNPsDetail",
+        "--anc_der_counts --haplogroup_paths --haplogroup_paths_detail\n"
+        "--der_snps --der_snps_detail --anc_snps --anc_snps_detail",
     )
     group.add_argument(
         "-c",
@@ -204,7 +204,8 @@ def get_command_line_args(set_defaults: bool = False) -> argparse.Namespace:
         "--snp_query",
         dest="query_snp_names",
         metavar="snp_names",
-        help="List phylogenetic path for each SNP in comma-separated list",
+        help="For each SNP in comma-separated list, output properties\n"
+        "and the phylogenetic path to the haplogroup it is associated with",
     )
     group.add_argument(
         "-pt",

yhaplo/sample.py

@@ -4,7 +4,6 @@
 * Sample
 * TextSample
 * VCFSample
-* AblockSample
 
 """
 

yhaplo/snp.py

@@ -125,6 +125,21 @@ def __str__(self) -> str:
             f"{self.ancestral}->{self.derived}"
         )
 
+    @property
+    def info(self) -> str:
+        """Return multiline summary of SNP."""
+
+        names = [name for name in self.name_list if name != self.label]
+        aliases_str = ", ".join(names) if names else "None"
+        info = (
+            f"Name: {self.label}\n"
+            f"YCC haplogroup: {self.node.label}\n"
+            f"GRCh37 position: {self.position:,}\n"
+            f"Mutation: {self.ancestral}->{self.derived}\n"
+            f"Aliases: {aliases_str}"
+        )
+        return info
+
     @property
     def str_with_all_names(self) -> str:
         """Return long string representation.
@@ -133,8 +148,8 @@ def str_with_all_names(self) -> str:
         plus a comma-separated list of names.
 
         """
-        names = ",".join(self.name_list)
-        str_with_all_names = f"{str(self)}     {names}"
+        names_str = ",".join(self.name_list)
+        str_with_all_names = f"{str(self)}     {names_str}"
         return str_with_all_names
 
     @property

yhaplo/tree.py

@@ -239,6 +239,7 @@ def query_snp_path(self, query_snp_name: str) -> None:
         snp = self.snp_dict.get(query_snp_name)
 
         if snp:
+            logger.info(f"{snp.info}\n")
             for node in snp.back_trace_path():
                 logger.info(node.str_simple)