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Makefile
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66 lines (43 loc) · 2.79 KB
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#####################################################################
## 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/