Removed command.py that was not supposed to be there

Makefile

@@ -54,7 +54,6 @@ test_val:
 # -----------------------------------------------------------------------
 #   experiments on real data (only Besnard)
 # -----------------------------------------------------------------------
-
 .PHONY: fast_real
 fast_real:
 	cd example && \
@@ -72,40 +71,11 @@ real:
 # -----------------------------------------------------------------------
 #   experiments on threshold choices
 # -----------------------------------------------------------------------
-
-.PHONY: analyses_seuils
-analyses_seuils:
-	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_seuils --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 16 --no-ne --no-hapc --ns 1000 && \
-	mv dag.dot daganalyses_seuils.dot
-
-.PHONY: analyses_everything_fast
-analyses_everything_fast:
-	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_everything_fast --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 16 --ns 100 --fast && \
-	mv dag.dot daganalyses_everything_fast.dot
-
-.PHONY: analyses_everything
-analyses_everything:
-	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_everything --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 16 --ns 100 && \
-	mv dag.dot daganalyses_everything.dot
-
-# -----------------------------------------------------------------------
-#   experiments on Ne values choices
-# -----------------------------------------------------------------------
-
-.PHONY: analyses_30Bloom_ne
-analyses_30Bloom_ne:
-	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30_ne --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 --ns 500 --only-sim && \
-	mv dag.dot daganalyses_tiragesBloomK30_ne.dot
-
-.PHONY: analyses_263Bloom_ne
-analyses_263Bloom_ne:
+.PHONY: analyses_we
+analyses_we:
 	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles_ne --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 --ns 500 --only-sim && \
-	mv dag.dot daganalyses_263SelectedProfiles_ne.dot
+	reviewphiltrans validation --outdir outdir_analyses_we --tree-dir trees_analyses_weekend --profile-fn aa_fitness/263SelectedProfiles.tsv --np 28 --ns 1000 && \
+	mv dag.dot daganalyses_we.dot
 
 # -----------------------------------------------------------------------
 #   Cleaning and formatting

example/trees_analyses_weekend/command.py

-
-from ete3 import Tree
-
-f_l=["./ensembl_3tr.nhx", "./cyp_coding.nhx"]
-
-def m_bl(t_n, m):
-    t=Tree(t_n)
-    for n in t.traverse():
-        n.dist = n.dist * m
-    out_n = t_n.replace(".nhx",".bl_%i.nhx" %(m))
-    t.write(format=1, features=["Condition","Transition"], outfile = out_n)
-
-list(map(lambda p: m_bl(p, 5), f_l))