gfam/Makefile at master · ntamas/gfam · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
#####################################################################
## Files and directories used in this script

CONFIG_FILE=gfam.cfg

GO_TREE_FILE=data/gene_ontology.obo

TAIR_DOMAINS_FILE=data/a.thaliana/tair9_iprscan1_0323_no_seg_no_coil.out.gz
TAIR_SEQUENCES_FILE=data/a.thaliana/TAIR9_pep_20090619_representative_gene_model.txt

INTERPRO_PARENT_CHILD_FILE=data/ParentChildTreeFile.txt
INTERPRO_GO_MAPPING_FILE=data/interpro2go

#####################################################################

PYTHON=python

.PHONY: clean

all: domain_architectures.zip

coverage: work/coverage_comparison.txt

overrep: work/overrepresentation_analysis.txt

work/gene_ids.txt: $(TAIR_SEQUENCES_FILE)
	$(PYTHON) -m gfam.scripts.extract_gene_ids -c $(CONFIG_FILE) $< >$@

work/filtered_assignments.txt: $(TAIR_DOMAINS_FILE) $(INTERPRO_PARENT_CHILD_FILE) work/gene_ids.txt bin/assignment_source_filter.py
	$(PYTHON) -m gfam.scripts.assignment_source_filter -c $(CONFIG_FILE) $< >$@

work/unassigned_fragments.tab: work/filtered_assignments.txt $(TAIR_SEQUENCES_FILE)
	$(PYTHON) -m gfam.scripts.find_unassigned -c $(CONFIG_FILE) <$< >$@

work/unassigned_fragments.ffa: work/unassigned_fragments.tab $(TAIR_SEQUENCES_FILE)
	$(PYTHON) -m gfam.scripts.seqslicer -c $(CONFIG_FILE) $< $(TAIR_SEQUENCES_FILE) >$@

work/unassigned_fragment_matches.blast: work/unassigned_fragments.ffa
	$(PYTHON) -m gfam.scripts.blast_all -c $(CONFIG_FILE) $< >$@

work/relevant_matches.blast: work/unassigned_fragment_matches.blast work/unassigned_fragments.ffa
	$(PYTHON) -m gfam.scripts.blast_filter -c $(CONFIG_FILE) $< >$@

work/relevant_matches_jaccard.tab: work/relevant_matches.blast
	$(PYTHON) -m gfam.scripts.jaccard -c $(CONFIG_FILE) $< >$@

work/relevant_matches_cca.tab: work/relevant_matches_jaccard.tab
	$(PYTHON) -m gfam.scripts.cca -c $(CONFIG_FILE) $< >$@

work/domain_architectures.tab: work/filtered_assignments.txt work/relevant_matches_cca.tab
	$(PYTHON) -m gfam.scripts.find_domain_arch -c $(CONFIG_FILE) $< work/relevant_matches_cca.tab >$@

work/overrepresentation_analysis.txt: work/domain_architectures.tab $(GO_TREE_FILE) $(INTERPRO_GO_MAPPING_FILE)
	$(PYTHON) -m gfam.scripts.overrep $(GO_TREE_FILE) $(INTERPRO_GO_MAPPING_FILE) $< >$@

work/coverage_comparison.txt: $(TAIR_DOMAINS_FILE) work/filtered_assignments.txt work/gene_ids.txt gfam/scripts/coverage.py
	$(PYTHON) -m gfam.scripts.coverage -c $(CONFIG_FILE) $< | sort >work/coverage_all.txt
	$(PYTHON) -m gfam.scripts.coverage -c $(CONFIG_FILE) work/filtered_assignments.txt | sort >work/coverage_selected.txt
	join -j 1 -t ' ' work/coverage_all.txt work/coverage_selected.txt | sed -e 's/ /\t/g' >$@

domain_architectures.zip: work/domain_architectures.tab work/overrepresentation_analysis.txt
	zip $@ work/domain_architecture* work/overrepresentation_analysis.txt

clean:
	rm -rf work/
	mkdir work/