proper testing: comparing using pandas

Dockerfile

@@ -8,11 +8,12 @@ FROM ubuntu:18.04
 # install prerequisites
 # - build-essential: for make
 # - libc-dev: contains argp
-# - zlib1g: zlib package
+# - python3, python3-pip, pandas: for testing
 RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y \
 		build-essential \
 		libc-dev \
-		#zlib1g-dev \
+		python3 \
+		python3-pip \
 	&& apt-get clean && rm -rf /var/lib/apt/lists/*
 
 # copy 
@@ -21,6 +22,9 @@ COPY . /astarix
 # set working directory
 WORKDIR /astarix
 
+RUN pip3 install pandas
+
 # compile and test
 RUN make && \
 	make test
+

Makefile

@@ -37,16 +37,13 @@ test: $(ASTARIXBIN)
 	# small
 	$(ASTARIXBIN) align-optimal -t 8 -v 2 -g $(DATADIR)/ecoli_head10000_linear/graph.gfa -q $(DATADIR)/ecoli_head10000_linear/illumina.fq -o $(TMPDIR)/ecoli_head10000_linear/astar-default
 	$(ASTARIXBIN) align-optimal -a dijkstra -g $(DATADIR)/ecoli_head10000_linear/graph.gfa -q $(DATADIR)/ecoli_head10000_linear/illumina.fq -o $(TMPDIR)/ecoli_head10000_linear/dijkstra-default
-	#python3 $(TESTSDIR)/compare_profilings.py $(TMPDIR)/ecoli_head10000_linear/astar-default/alignments.tsv $(TMPDIR)/ecoli_head10000_linear/dijkstra-default/alignments.tsv
-
-	#$(ASTARIXBIN) align-optimal -g $(DATADIR)/ecoli_head10000_linear/graph.gfa -q $(DATADIR)/illumina.fq -o $(TMPDIR)/ecoli_head10000_linear/astar-default
-	#$(ASTARIXBIN) align-optimal -a astar-prefix -g $(DATADIR)/ecoli_head10000_linear/graph.gfa -q $(DATADIR)/ecoli_head10000_linear/illumina.fq -D 5 -f 0 -d 10 -c 3 -M 0 -e 0 -S 1 -G 1 -o $(TMPDIR)/ecoli_head10000_linear/astar-custom
+	python3 $(TESTSDIR)/compare_profilings.py $(TMPDIR)/ecoli_head10000_linear/astar-default/alignments.tsv $(TMPDIR)/ecoli_head10000_linear/dijkstra-default/alignments.tsv
 
 bigtest:
 	# 10000 reads
 	$(ASTARIXBIN) align-optimal -t 8 -g $(DATADIR)/ecoli_head1000000_linear/graph.gfa -q $(DATADIR)/ecoli_head1000000_linear/illumina.fq -o $(TMPDIR)/ecoli_head1000000_linear/astar-default
 	$(ASTARIXBIN) align-optimal -a dijkstra -g $(DATADIR)/ecoli_head1000000_linear/graph.gfa -q $(DATADIR)/ecoli_head1000000_linear/illumina.fq -o $(TMPDIR)/ecoli_head1000000_linear/dijkstra-default
-	#python3 $(TESTSDIR)/compare_profilings.py $(TMPDIR)/ecoli_head1000000_linear/astar-default/alignments.tsv $(TMPDIR)/ecoli_head1000000_linear/dijkstra-default/alignments.tsv
+	python3 $(TESTSDIR)/compare_profilings.py $(TMPDIR)/ecoli_head1000000_linear/astar-default/alignments.tsv $(TMPDIR)/ecoli_head1000000_linear/dijkstra-default/alignments.tsv
 
 eval: $(ASTARIXBIN)
 	$(shell mkdir -p $(TMPDIR))

README.md

@@ -30,6 +30,7 @@ In order to compile AStarix, you will need to first install:
 
 * [argp](https://www.gnu.org/software/libc/manual/html_node/Argp.html) –
   argument parsing library
+* (optional) [pandas](https://pandas.pydata.org/) – dataframe library used for testing and evalutaions
 
 We show how to install them in the [Dockerfile](./Dockerfile).
 Other third-party libraries are located in the `/ext` directory and their own licenses apply.