Merge pull request #17 from karel-brinda/proc_subst

Fix tests

Author: karel-brinda

tests/00_data/.gitignore

@@ -0,0 +1 @@
+*.fa

tests/00_data/Makefile

@@ -0,0 +1,46 @@
+.PHONY: all help clean cleanall view
+
+SHELL=/usr/bin/env bash -eo pipefail
+
+.SECONDARY:
+
+.SUFFIXES:
+
+FASTAS=001334.fa 101058.fa 203692.fa 302649.fa 403790.fa
+
+##############
+## Commands ##
+##############
+
+all: test_spneumo.tar.xz
+
+test_spneumo.tar.xz: $(FASTAS)
+	tar -cvf - $? \
+		| xz -T1 -9 \
+		> $@.tmp
+	mv $@.tmp $@
+
+%.fa:
+	curl -L "https://github.com/c2-d2/rase-db-spneumoniae-sparc/raw/master/isolates/$*.fa" \
+		| seqtk seq \
+		> $@.tmp
+	mv $@.tmp $@
+
+
+help: ## Print help messages
+	@echo -e "$$(grep -hE '^\S*(:.*)?##' $(MAKEFILE_LIST) \
+		| sed \
+			-e 's/:.*##\s*/:/' \
+			-e 's/^\(.*\):\(.*\)/   \\x1b[36m\1\\x1b[m:\2/' \
+			-e 's/^\([^#]\)/\1/g' \
+			-e 's/: /:/g' \
+			-e 's/^#\(.*\)#/\\x1b[90m\1\\x1b[m/' \
+		| column -c2 -t -s : )"
+
+clean: ## Clean
+	rm -fv *.fa
+
+cleanall: clean ## Clean all
+	rm -fv *.tar.xz
+
+view: ## View output

tests/00_data/test_spneumo.tar.xz

@@ -1,2 +1,3 @@
+file_list.txt
 *.fa
 *.nw

tests/02_simple_tree/.gitignore

@@ -6,20 +6,39 @@ SHELL=/usr/bin/env bash -eo pipefail
 
 .SUFFIXES:
 
-FASTAS=001334.fa 101058.fa 203692.fa 302649.fa 403790.fa
+FASTAS=$(shell tar -tf test_spneumo.tar.xz)
 
-##############
-## Commands ##
-##############
+###################
+## Compare trees ##
+###################
+
+all: tree.default.nw tree.file_list.nw tree.precomputed.newick
+	diff tree.default.nw tree.precomputed.newick
+	diff tree.file_list.nw tree.precomputed.newick
+
+###################################
+# Different ways to compute trees #
+###################################
 
-all: tree.nw
+tree.default.nw: file_list.txt
+	../../attotree/attotree.py $(shell cat $<) > "$@.tmp"
+	mv "$@.tmp" "$@"
 
-tree.nw: $(FASTAS)
-	../../attotree/attotree.py $? > $@.tmp
-	mv $@.tmp $@
+tree.file_list.nw: file_list.txt
+	../../attotree/attotree.py -L "$<"  > "$@.tmp"
+	mv "$@.tmp" "$@"
+
+tree.precomputed.newick: tree.default.nw
+	cp $< $@
+
+##############
+# Input data #
+##############
 
-%.fa:
-	curl -L "https://github.com/c2-d2/rase-db-spneumoniae-sparc/raw/master/isolates/$*" > $@
+file_list.txt: test_spneumo.tar.xz
+	tar xvf $<
+	tar -tf $< > file_list.txt.tmp
+	mv file_list.txt.tmp file_list.txt
 
 help: ## Print help messages
 	@echo -e "$$(grep -hE '^\S*(:.*)?##' $(MAKEFILE_LIST) \
@@ -32,8 +51,9 @@ help: ## Print help messages
 		| column -c2 -t -s : )"
 
 clean: ## Clean
-	rm -fv *.nw
+	rm -f *.nw *.tmp
 
 cleanall: clean ## Clean all
+	rm -f file_list.txt *.fa
 
 view: ## View output

tests/02_simple_tree/Makefile

@@ -0,0 +1 @@
+../00_data/test_spneumo.tar.xz

tests/02_simple_tree/test_spneumo.tar.xz

@@ -0,0 +1 @@
+((203692:0.00537,001334:0.00473):0.00060,(302649:0.00543,101058:0.00531):0.00062,403790:0.01403);