diff options
author | Martin Czygan <martin.czygan@gmail.com> | 2021-05-19 22:33:01 +0200 |
---|---|---|
committer | Martin Czygan <martin.czygan@gmail.com> | 2021-05-19 22:33:01 +0200 |
commit | 9cdef6270986b48746fa7e4a610f1bbeb2ed8d3d (patch) | |
tree | d14908ef8fa432608f8ef1315dc1c09b7c19be42 /python | |
parent | 19ab14391f64ed385d05a371b1bb9547cf408b23 (diff) | |
download | refcat-9cdef6270986b48746fa7e4a610f1bbeb2ed8d3d.tar.gz refcat-9cdef6270986b48746fa7e4a610f1bbeb2ed8d3d.zip |
tasks: add RefsMapped
Diffstat (limited to 'python')
-rw-r--r-- | python/refcat/tasks.py | 26 |
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. |