/
Makefile
39 lines (26 loc) · 968 Bytes
/
Makefile
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CTXDIR=../..
DNACAT=$(CTXDIR)/libs/seq_file/bin/dnacat
BIOINF=$(CTXDIR)/libs/bioinf-perl
CTX2DOT=$(CTXDIR)/scripts/cortex_to_graphviz.pl
CTX=$(CTXDIR)/bin/ctx31
K=9
all: test
seq.fa:
$(DNACAT) -F -n 1001 > seq.fa
seq.k$(K).ctx: seq.fa
$(CTX) build -m 1M -k $(K) --sample MrsSample --seq seq.fa $@
seq.k$(K).ctp.gz: seq.k$(K).ctx seq.fa
$(CTX) thread -m 1M --seq seq.fa --out $@ seq.k$(K).ctx
contigs.fa: seq.k$(K).ctx seq.k$(K).ctp.gz
$(CTX) contigs --out $@ -p seq.k$(K).ctp.gz seq.k$(K).ctx
contigs.rmdup.fa: contigs.fa
$(CTX) rmsubstr $< > $@
seq.k$(K).pdf: seq.k$(K).ctx
$(CTX2DOT) --simplify $< | dot -Tpdf > $@
plots: seq.k$(K).pdf
test: seq.fa contigs.fa contigs.rmdup.fa
$(BIOINF)/sim_mutations/sim_substrings.pl $(K) 0.1 contigs.fa seq.fa
$(BIOINF)/sim_mutations/sim_substrings.pl $(K) 0.1 contigs.rmdup.fa seq.fa
clean:
rm -rf seq.fa seq.k$(K).ctx seq.k$(K).ctp.gz contigs.fa contigs.rmdup.fa seq.k$(K).pdf
.PHONY: all clean test plots