update makefile

Makefile

@@ -28,7 +28,7 @@ push_docker:
 	done
 
 # -----------------------------------------------------------------------
-#   Tests and experiments
+#   Tests
 # -----------------------------------------------------------------------
 .PHONY: test_simu
 test_simu:
@@ -51,24 +51,55 @@ test_val:
 	mv dag.dot dagtest_val.dot && \
 	dot -Tsvg dagtest_val.dot -o dagtest_val.svg
 
+# -----------------------------------------------------------------------
+#   experiments on real data (only Besnard)
+# -----------------------------------------------------------------------
+
+.PHONY: fast_real
+fast_real:
+	cd example && \
+	reviewphiltrans detection --outdir outdir_real_data --indir real_data --fast --np 4 && \
+	mv dag.dot dagtest_real.dot && \
+	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf
+
 .PHONY: real
 real:
 	cd example && \
-	reviewphiltrans detection --outdir outdir_real_data --indir real_data --preview --np 4 && \
+	reviewphiltrans detection --outdir outdir_real_data --indir real_data --np 4 && \
 	mv dag.dot dagtest_real.dot && \
 	dot -Tpdf dagtest_real.dot -o dagtest_real.pdf
 
-.PHONY: analyses_30Bloom
-analyses_30Bloom:
+# -----------------------------------------------------------------------
+#   experiments on threshold choices
+# -----------------------------------------------------------------------
+
+.PHONY: analyses_30Bloom_t
+analyses_30Bloom_t:
+	cd example && \
+	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30_t --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 --no-ne --no-hapc --ns 500 && \
+	mv dag.dot daganalyses_tiragesBloomK30_t.dot
+
+.PHONY: analyses_263Bloom_t
+analyses_263Bloom_t:
+	cd example && \
+	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles_t --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 --no-ne --no-hapc --ns 500 && \
+	mv dag.dot daganalyses_263SelectedProfiles_t.dot
+
+# -----------------------------------------------------------------------
+#   experiments on Ne values choices
+# -----------------------------------------------------------------------
+
+.PHONY: analyses_30Bloom_ne
+analyses_30Bloom_ne:
 	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30 --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 && \
-	mv dag.dot daganalyses_tiragesBloomK30.dot
+	reviewphiltrans validation --outdir outdir_analyses_tiragesBloomK30_ne --tree-dir trees4analyses --profile-fn aa_fitness/tiragesBloomK30.tsv --np 4 --fast --ns 500 && \
+	mv dag.dot daganalyses_tiragesBloomK30_ne.dot
 
-.PHONY: analyses_263Bloom
-analyses_263Bloom:
+.PHONY: analyses_263Bloom_ne
+analyses_263Bloom_ne:
 	cd example && \
-	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 && \
-	mv dag.dot daganalyses_263SelectedProfiles.dot
+	reviewphiltrans validation --outdir outdir_analyses_263SelectedProfiles_ne --tree-dir trees4analyses --profile-fn aa_fitness/263SelectedProfiles.tsv --np 4 --fast --ns 500 && \
+	mv dag.dot daganalyses_263SelectedProfiles_ne.dot
 
 # -----------------------------------------------------------------------
 #   Cleaning and formatting