Re-factored the repository to automatically calculate QC on every flowcell. I also...

diff --git a/htswanalysis/scripts/Flowcell_QC_Makefile b/htswanalysis/scripts/Flowcell_QC_Makefile
index 8f91e433a4fe9b836492fde10170e6a04ebdacb6..1c94fd02691bb0de73d9d13dd582925214297dec 100644 (file)
--- a/htswanalysis/scripts/Flowcell_QC_Makefile
+++ b/htswanalysis/scripts/Flowcell_QC_Makefile
@@ -5,11 +5,15 @@ FLOWCELL=$(shell pwd | awk -F/ '{print $$NF}')
 FILES=$(shell ls -1d *.align*.txt)
 QPCR_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.qPCR/)
 COUNT_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.count/)
+CMPLX_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.complexity/)
 PROFILE_FILES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.profile/)
 PROFILE_IMAGES=$(shell ls -1d *.align*.txt | sed -e s/txt/txt.profile.png/)
 PERCENT_BASE_IMAGES=$(shell ls -1d *.pf.txt.gz | sed -e s/pf.txt.gz/percent_base.png/)
 
-all: $(QPCR_FILES) $(PROFILE_FILES) $(PROFILE_IMAGES) $(PERCENT_BASE_IMAGES) $(COUNT_FILES) $(FILES) $(FLOWCELL)_qPCR_summary.txt $(FLOWCELL)_qPCR_summary.html $(FLOWCELL)_LibraryInfo.xml $(FLOWCELL)_SequencingSummary.html $(FLOWCELL)_QC_Summary.html
+all: $(QPCR_FILES) $(PROFILE_FILES) $(CMPLX_FILES) $(PROFILE_IMAGES) $(PERCENT_BASE_IMAGES) $(COUNT_FILES) $(FILES) $(FLOWCELL)_qPCR_summary.txt $(FLOWCELL)_qPCR_summary.html $(FLOWCELL)_LibraryInfo.xml $(FLOWCELL)_SequencingSummary.html $(FLOWCELL)_QC_Summary.html
+
+%.txt.complexity: %.txt
+       $(ROOT_DIR)/bin/complexity_count `basename $<` $< > $@
 
 %.txt.count: %.txt
        grep -v contam $< | awk '{if(NF > 3) {print $$1} }' | wc -l > $@;
@@ -44,5 +48,5 @@ $(FLOWCELL)_LibraryInfo.xml: $(COUNT_FILES)
 $(FLOWCELL)_SequencingSummary.html: $(FLOWCELL)_LibraryInfo.xml
        $(EXPTRACK_DIR)/scripts/SummarizeLibrary.pm $< > $@
 
-$(FLOWCELL)_QC_Summary.html: $(FLOWCELL)_SequencingSummary.html $(FLOWCELL)_qPCR_summary.html $(PROFILE_FILES)
+$(FLOWCELL)_QC_Summary.html: $(FLOWCELL)_SequencingSummary.html $(FLOWCELL)_qPCR_summary.html $(PROFILE_IMAGES) $(PERCENT_BASE_IMAGES)
        $(EXPTRACK_DIR)/scripts/WriteQCSummary.pm $(FLOWCELL)_LibraryInfo.xml $(FLOWCELL)_qPCR_summary.txt > $@;

diff --git a/htswanalysis/scripts/LibrariesMakefile b/htswanalysis/scripts/LibrariesMakefile
index 0305e8fbb241a8e5d690ed28934e5d2f02c897ed..71abc370fd67238b5e147c59d1351470b082804a 100644 (file)
--- a/htswanalysis/scripts/LibrariesMakefile
+++ b/htswanalysis/scripts/LibrariesMakefile
@@ -1,11 +1,5 @@
 #
-# Makefile to bring new flowcells ointo the repository. A few bits of computation are done upfront:
-#
-#  qPCR -- checks in-silico to see if the lane looks like a factor we know about
-#  count -- counts the number of (not adapter) aligned reads in the lane
-#  complexity -- looks for isolated peaks that are a symptom of low-complexity libraries (or sequencing of a restriction enzyme)
-#  profile -- profile of read density relative to the TSS
-#  libfiles -- the configure files for the libraries
+# Makefile to bring new flowcells into the repository, calculating QC for each of them.
 #
 # Once the makefile has run once (please, for your sanity, use make -j N (where N is the number of CPU cores you have),
 # then you need to run it again to actually make the libraries proper. This will be (needs to be fixed).
@@ -24,43 +18,25 @@ HTML_DIR=/Library/WebServer/Documents/SequencingSummaries
 
 # Error messages are collected so as not to bug the user. (if there are no matching files, ls errors.)
 FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMakefile.err)
-QPCR_FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMakefile.err | sed -e s/txt/txt.qPCR/)
-COUNT_FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMakefile.err | sed -e s/txt/txt.count/)
-CMPLX_FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMakefile.err | sed -e s/txt/txt.complexity/)
-PROFILE_FILES=$(shell ls -1d $(DATA_DIR)/Flowcells/**/*.align*.txt 2>> LibrariesMakefile.err | sed -e s/txt/txt.profile/)
+QC_FILES=$(shell ls -1d ~Data/Flowcells/**/ | awk -F/ '{print $$0"/"$$(NF-1)"_QC_Summary.html"}' )
 LIBFILES=$(shell ls -1d $(DATA_DIR)/Libraries/.*.config 2>> LibrariesMakefile.err | sed -e s/config/txt/ -e "s/\/\./\//")
 
-all: $(QPCR_FILES) $(COUNT_FILES) $(FILES) $(DATA_DIR)/qPCR_summary.txt $(DATA_DIR)/LibraryInfo.xml $(LIBFILES) $(DATA_DIR)/SequencingSummary.html Distribute
-
-%.txt.complexity: %.txt
-       $(ROOT_DIR)/bin/complexity_count `basename $<` $< > $@
-
-%.txt.count: %.txt
-       grep -v contam $< | awk '{if(NF > 3) {print $$1} }' | wc -l > $@;
+all: $(QC_FILES) $(FILES) $(DATA_DIR)/LibraryInfo.xml $(LIBFILES) $(DATA_DIR)/SequencingSummary.html Distribute
 
-%.txt.qPCR: %.txt
-       $(ROOT_DIR)/bin/qPCR $(subst .txt.qPCR,.txt,$@) $(ROOT_DIR)/reference_data/GenericBackground $(ROOT_DIR)/reference_data/qPCR_Tests/ | sort -k 2 -g -r > $@
-
-%.txt.profile: %.txt
-       $(ROOT_DIR)/profile_reads/profile_reads_against_features `echo $@ | sed -e s/\.profile//` $(ROOT_DIR)/reference_data/`basename $@ | awk -F\. '{ print $$3 }'`_tx_start_sites > $@
-       $(ROOT_DIR)/profile_reads/profile_to_svg.pm $@ > $@.svg
+$(QC_FILES):
+       cd $(DATA_DIR)/Flowcells/`basename $@ | awk -F_ '{print $$1}'` && $(MAKE) -f $(ROOT_DIR)/scripts/Flowcell_QC_Makefile
 
 $(DATA_DIR)/Libraries/%.txt: $(DATA_DIR)/Libraries/.%.config | LibraryInfo.xml
        cat `cat $<` > $@;
 
-$(DATA_DIR)/qPCR_summary.txt: $(QPCR_FILES)
-       rm -f $@;
-       for f in $^; do echo `echo $$f`       `cat $$f | head -n 1` >> $@; done;
-       cat $@ | sort -k 2,1 -g -r > t && mv t $@;
-
-$(DATA_DIR)/LibraryInfo.xml: $(COUNT_FILES) $(CMPLX_FILES)
+$(DATA_DIR)/LibraryInfo.xml: $(QC_FILES)
        $(ROOT_DIR)/scripts/CollectLibraries.pm `ls $(DATA_DIR)/Flowcells/**/*.align*.txt` > $@;
        $(ROOT_DIR)/scripts/RecompileLibraries.pm $@ $(DATA_DIR)
 
 $(DATA_DIR)/SequencingSummary.html: $(DATA_DIR)/LibraryInfo.xml
        $(ROOT_DIR)/scripts/SummarizeLibrary.pm $< > $@;
 
-Distribute: SequencingSummary.html qPCR_summary.txt
+Distribute: SequencingSummary.html
        cp $^ $(HTML_DIR);
 
 Libraries: $(LIBFILES)