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Makefile_targetSelectivity
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Makefile_targetSelectivity
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################################################################################
# (C) 2016 Tyler W. H. Backman
# Tables and figures for Protein Target Diversity, Target Selectivity Distribution
# and Selectivity by Target Pfam Domains
################################################################################
# get go terms for all targets
working/uniprotGOannotations.csv: src/uniprot_annotator.py $(databaseFile) working/gene_association.goa_uniprot
$< --database=$(databaseFile) --uniprot=working/gene_association.goa_uniprot --outfile=$@
# build GI->GO annotations table
working/targetGOannotations.csv: src/targetGOannotations.R working/uniprotGOannotations.csv $(databaseFile)
$^ $@
# find GO slim annotations for individual targets
working/targetGOslimAnnotations.csv: src/clusterGOslimAnnotations.R working/targetGOannotations.csv working/goslim_generic.obo
$^ $@
# plot distribution of domain activity
working/compoundsByDomain.pdf: src/compounds_by_domain.R working/cidsVStargets.RData working/drugbank_links.csv $(databaseFile) working/Pfam-A.clans.tsv working/humanDomainsTwoCols working/PfamResidueLengths.tab
$^ $(cores) $@
# compute distribution of target selectivity values
working/selectivityCountsIndividual.txt: src/computeSelectivity.R $(databaseFile) working/highlyScreenedCids.txt
$^ $@ $(cores) FALSE keepOne
# compute distribution of kClust selectivity values
working/selectivityCountskClust.txt: src/computeSelectivity.R $(databaseFile) working/highlyScreenedCids.txt
$^ $@ $(cores) kClust keepOne
# compute distribution of domain selectivity values
working/selectivityCountsdomains.txt: src/computeSelectivity.R $(databaseFile) working/highlyScreenedCids.txt
$^ $@ $(cores) domains keepOne
# plot distribution of target selectivity
working/targetSelectivitySequenceClusters.pdf: src/targetSelectivity.R working/selectivityCountsIndividual.txt working/selectivityCountskClust.txt working/selectivityCountsdomains.txt working/drugbank_links.csv
$^ $@
# compute target selectivity on a per-domain basis
working/targetSelectivityByDomain.tab: src/targetSelectivityByDomain.R $(databaseFile) working/highlyScreenedCids.txt working/drugbank_links.csv
$^ $@ $(cores) keepOne
# compute heavy atom (non hydrogen) count
working/heavycount.txt: src/computeMoleculeSize.R working/bioassayCompounds
$^ $@ $(cores)
# plot heavy atom count distribution vs selectivity
working/plotSelectivityBySize.pdf: src/plotSelectivityBySize.R working/selectivityCountskClust.txt working/drugbank_links.csv working/heavycount.txt working/highlyScreenedCids.txt working/activeCids.txt $(databaseFile)
$^ $@
# Fit functions to target selectivity function
# plot distribution of target selectivity
working/selectivityFit.pdf: src/stretchedExponential.R working/drugbank_links.csv
$^ $@
# compute MF GO slim for each domain
working/domainGOslimAnnotations.csv: src/pfamGOslimAnnotations.R working/pfam2go working/goslim_generic.obo
$^ $@
# make latex table of target selectivity on a per-domain basis
working/targetSelectivityByDomainFreq.tex: src/targetSelectivityByDomainTable.R working/targetSelectivityByDomain.tab working/Pfam-A.clans.tsv $(databaseFile) working/domainGOslimAnnotations.csv working/humanDomainsTwoCols working/targetGOslimAnnotations.csv working/PfamResidueLengths.tab
$^ $@