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xapple · Aug 12, 2015 · 8c9f7c9 · 8c9f7c9
1 parent 47cd17d
commit 8c9f7c9
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Showing 2 changed files with 12 additions and 4 deletions.
diff --git a/gefes/annotation/prodigal.py b/gefes/annotation/prodigal.py
@@ -41,10 +41,10 @@ def run(self, cpus=None):
         # Variable threads #
         if cpus is None: cpus = num_processors
         # Run it #
-        sh.prokka('-i', self.contig.fasta,
-                  '-o', self.p.gbk,
-                  '-a', self.p.faa,
-                  '-p', 'anon')
+        sh.prodigal('-i', self.contig.fasta,
+                   '-o', self.p.gbk,
+                   '-a', self.p.faa,
+                   '-p', 'anon')
 
     @property_cached
     def results(self):

diff --git a/scripts/projects/soda_rerun/run.py b/scripts/projects/soda_rerun/run.py
@@ -129,6 +129,14 @@
 proj.runner.run_slurm(steps=['assembly_81.results.binner.run'], job_name=proj.name+'_bin_81', **params)
 proj.runner.run_slurm(steps=['merged.results.binner.run'],      job_name=proj.name+'_bin_04', **params)
 
+################################## Prokka #####################################
+print "Prokka for project '%s', assembly '%s'" % (proj.name, proj.merged)
+for c in tqdm(proj.merged.results.contigs): c.annotation.run(cpus=4)
+
+################################## Prodigal #####################################
+print "Prokka for project '%s', assembly '%s'" % (proj.name, proj.merged)
+for c in tqdm(proj.merged.results.contigs): c.proteins.run()
+
 ################################## Plots ######################################
 for s in tqdm(samples):
     print "Plots for sample '%s'" % s.name