tasks: add RefsMapped

1 files changed, 26 insertions, 0 deletions

diff --git a/python/refcat/tasks.py b/python/refcat/tasks.py
index b00302e..6d7bf56 100644
--- a/python/refcat/tasks.py
+++ b/python/refcat/tasks.py
@@ -543,6 +543,32 @@ class FatcatMapped(Refcat):
         return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd)
 
 
+class RefsMapped(Refcat):
+    """
+    Apply mapper on refs.
+    """
+    mapper = luigi.Parameter(default="ts", description="mapper short name")
+
+    def requires(self):
+        return RefsToRelease()
+
+    def run(self):
+        output = shellout("""
+                          zstdcat -T0 {input} |
+                          skate-map -m {mapper} -skip-on-empty 1 |
+                          LC_ALL=C sort -T {tmpdir} -k1,1 -S25% --parallel 4 |
+                          zstd -T0 -c > {output}
+                          """,
+                          n=self.n,
+                          mapper=self.mapper,
+                          tmpdir=self.tmpdir,
+                          input=self.input().path)
+        luigi.LocalTarget(output).move(self.output().path)
+
+    def output(self):
+        return luigi.LocalTarget(path=self.path(ext="tsv.zst"), format=Zstd)
+
+
 class BrefZipDOI(Refcat):
     """
     Run skate-reduce from two files.