add yeast mixture eid summary results and fig

Add a script to compile raw results into summary formats. Include new python script for drawing out line plot of summarized results.

Author: owlang

paper/SyntheticEpitope/job/compile_mix_results.sh

@@ -0,0 +1,74 @@
+#!/bin/bash
+
+set -exo
+
+# FIRST CHANGE PATH TO EXECUTE
+WRK=/path/to/GenoPipe/paper/SyntheticEpitope
+cd $WRK
+
+# CALCULATE=scripts/calculate_detection_Stats.pl
+TALLY=scripts/analyze_eid_results.py
+BAR=scripts/build_barplots.py
+LINE=scripts/build_lineplots.py
+
+REF="sacCer3"
+DEPTH="1M"
+LENGTH="500"
+EPITOPE=R$LENGTH
+AFACTOR=Rap1
+BFACTOR=Reb1
+SUMMARY=results/MixSummaryReport_$REF\_$DEPTH.txt
+RSUMMARY=results/MixRuntimeSummaryReport_$REF\_$DEPTH.txt
+[ -f $SUMMARY ] && rm $SUMMARY
+[ -f $RSUMMARY ] && rm $RSUMMARY
+
+EPITOPE=R$LENGTH
+for PER in 90 80 70 60 50 40 30 20 10
+do
+	CATRAW=results/mix_yeast/mix_yeast_$DEPTH\_$PER\_$AFACTOR\_$BFACTOR-all-IDs.tab
+	head -n 9999 results/mix_yeast/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/ID/*.tab > $CATRAW
+	# perl $CALCULATE $CATRAW $PROTEIN RANDOM_SEQ_$LENGTH >> $SUMMARY/$DEPTH\_$EPITOPE\_$PROTEIN\_summary.txt
+	python $TALLY -i results/mix_yeast/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/ID/ -e RANDOM_SEQ_$LENGTH -t $AFACTOR \
+		| sort > A-temp
+	python $TALLY -i results/mix_yeast/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/ID/ -e RANDOM_SEQ_$LENGTH -t $BFACTOR \
+		| sort > B-temp
+	paste A-temp B-temp >> $SUMMARY
+
+	RUNTIMES=results/mix_yeast/mix_yeast_$DEPTH\_$PER\_$AFACTOR\_$BFACTOR-all-runtimes.tab
+	grep 'finished in' results/mix_yeast/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/runtime/*.runtime > $RUNTIMES
+	paste <(cut -d":" -f1 $RUNTIMES) <(awk '{FS=" "}{OFS="\t"}{print $2,$6}' $RUNTIMES) >> $RSUMMARY
+done
+
+# Build yeast figures
+python $LINE -i $SUMMARY -o results/ID-Mix-tally_$REF\_$DEPTH.png
+
+REF="hg19"
+DEPTH="20M"
+LENGTH="500"
+EPITOPE=R$LENGTH
+AFACTOR=CTCF
+BFACTOR=POLR2H
+SUMMARY=results/MixSummaryReport_$REF\_$DEPTH.txt
+RSUMMARY=results/MixRuntimeSummaryReport_$REF\_$DEPTH.txt
+[ -f $SUMMARY ] && rm $SUMMARY
+[ -f $RSUMMARY ] && rm $RSUMMARY
+
+EPITOPE=R$LENGTH
+for PER in 90 80 70 60 50 40 30 20 10
+do
+	CATRAW=results/mix_human/mix_human_$DEPTH\_$PER\_$AFACTOR\_$BFACTOR-all-IDs.tab
+	head -n 9999 results/mix_human/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/ID/*.tab > $CATRAW
+	# perl $CALCULATE $CATRAW $PROTEIN RANDOM_SEQ_$LENGTH >> $SUMMARY/$DEPTH\_$EPITOPE\_$PROTEIN\_summary.txt
+	python $TALLY -i results/mix_human/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/ID/ -e RANDOM_SEQ_$LENGTH -t $AFACTOR \
+		| sort > A-temp
+	python $TALLY -i results/mix_human/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/ID/ -e RANDOM_SEQ_$LENGTH -t $BFACTOR \
+		| sort > B-temp
+	paste A-temp B-temp >> $SUMMARY
+
+	RUNTIMES=results/mix_human/mix_human_$DEPTH\_$PER\_$AFACTOR\_$BFACTOR-all-runtimes.tab
+	grep 'finished in' results/mix_human/$DEPTH/$PER\_$AFACTOR\_$BFACTOR/runtime/*.runtime > $RUNTIMES
+	paste <(cut -d":" -f1 $RUNTIMES) <(awk '{FS=" "}{OFS="\t"}{print $2,$6}' $RUNTIMES) >> $RSUMMARY
+done
+
+# Build human figures
+python $LINE -i $SUMMARY -o results/ID-Mix-tally_$REF\_$DEPTH.png