seashell-cli 0.1.1__tar.gz → 0.1.2__tar.gz

{seashell_cli-0.1.1 → seashell_cli-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seashell-cli
-Version: 0.1.1
+Version: 0.1.2
 Summary: Seashell — Genomic data, compressed and queryable
 License: Proprietary
 Project-URL: Homepage, https://seashell.bio

{seashell_cli-0.1.1 → seashell_cli-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "seashell-cli"
-version = "0.1.1"
+version = "0.1.2"
 description = "Seashell — Genomic data, compressed and queryable"
 readme = "README.md"
 license = {text = "Proprietary"}

seashell_cli-0.1.2/seashell/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.2"

{seashell_cli-0.1.1 → seashell_cli-0.1.2}/seashell/display.py

@@ -172,13 +172,53 @@ def _print_variants(result, action, latency):
 
 
 def _print_diff(result, latency):
-    print("\n  %s vs %s" % (result.get("patient_a", "?"), result.get("patient_b", "?")))
-    print("  Only in A: %s variants" % result.get("only_in_a", "?"))
-    print("  Only in B: %s variants" % result.get("only_in_b", "?"))
-    print("  Shared:    %s variants" % result.get("shared", "?"))
+    a = result.get("patient_a", "?")
+    b = result.get("patient_b", "?")
+    shared_count = result.get("shared_count", 0)
+    unique_a_count = result.get("unique_to_a_count", 0)
+    unique_b_count = result.get("unique_to_b_count", 0)
+    truncated = result.get("truncated", False)
+
+    print("\n  %s vs %s" % (a, b))
+    print("  %s %12s variants" % ("Only in " + a + ":", "{:,}".format(unique_a_count)))
+    print("  %s %12s variants" % ("Only in " + b + ":", "{:,}".format(unique_b_count)))
+    print("  %s %12s variants" % ("Shared:" + " " * (len(a) + len(b) - 1), "{:,}".format(shared_count)))
+
+    # Show a sample of shared variants if any
+    shared_sample = result.get("shared", [])
+    if shared_sample:
+        shown = len(shared_sample)
+        label = "first %d" % shown if truncated else "all %d" % shown
+        print("\n  Shared variants (%s):" % label)
+        header = "  %-8s %12s %-6s %-6s" % ("CHROM", "POS", "REF", "ALT")
+        has_gene = any("gene" in r for r in shared_sample)
+        if has_gene:
+            header += " %-12s" % "GENE"
+        print(header)
+        print("  %s" % ("-" * (len(header) - 2)))
+        for r in shared_sample[:25]:  # show at most 25 in table
+            line = "  %-8s %12s %-6s %-6s" % (
+                r.get("chrom", ""), r.get("pos", 0),
+                _truncate(r.get("ref", ""), 6),
+                _truncate(r.get("alt", ""), 6))
+            if has_gene:
+                line += " %-12s" % r.get("gene", "")
+            print(line)
+        if shown > 25:
+            print("  ... (%d more not shown)" % (shown - 25))
+
     print("\n  %s ms" % latency)
 
 
+def _truncate(s, n):
+    """Truncate a string to n chars with ellipsis."""
+    if not isinstance(s, str):
+        return str(s)
+    if len(s) <= n:
+        return s
+    return s[:n - 1] + "…"
+
+
 def _print_pca(result, latency):
     components = result.get("components", [])
     print("\n  PCA (%s components, %s patients)\n" % (

{seashell_cli-0.1.1 → seashell_cli-0.1.2}/seashell_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seashell-cli
-Version: 0.1.1
+Version: 0.1.2
 Summary: Seashell — Genomic data, compressed and queryable
 License: Proprietary
 Project-URL: Homepage, https://seashell.bio

{seashell_cli-0.1.1 → seashell_cli-0.1.2}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = seashell-cli
-version = 0.1.1
+version = 0.1.2
 description = Seashell — Genomic data, compressed and queryable
 long_description = file: README.md
 long_description_content_type = text/markdown

seashell_cli-0.1.1/seashell/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.1.1"