minor script updates

mix_fastq.sh
- uncomment intermediate file cleanup
compile_mix_results.sh
- add "-y" flag to yeast figure
- switch human mix depth to 50M (from 20M)
- reduce redundant EPITOPE env var declarations
run_mix_yeast.sh/run_mix_human.sh
- add directory check and initializations
build_lineplots.py
- add comments with code to stretch figure to edges of plot

Author: owlang

paper/SyntheticEpitope/job/compile_mix_results.sh

@@ -11,18 +11,18 @@ TALLY=scripts/analyze_eid_results.py
 BAR=scripts/build_barplots.py
 LINE=scripts/build_lineplots.py
 
-REF="sacCer3"
-DEPTH="1M"
 LENGTH="500"
 EPITOPE=R$LENGTH
+
+REF="sacCer3"
+DEPTH="1M"
 AFACTOR=Rap1
 BFACTOR=Reb1
 SUMMARY=results/MixSummaryReport_$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
@@ -40,10 +40,10 @@ do
 done
 
 # Build yeast figures
-python $LINE -i $SUMMARY -o results/ID-Mix-tally_$REF\_$DEPTH.png
+python $LINE -i $SUMMARY -y -o results/ID-Mix-tally_$REF\_$DEPTH.png
 
 REF="hg19"
-DEPTH="20M"
+DEPTH="50M"
 LENGTH="500"
 EPITOPE=R$LENGTH
 AFACTOR=CTCF
@@ -53,7 +53,6 @@ RSUMMARY=results/MixRuntimeSummaryReport_$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

paper/SyntheticEpitope/job/run_mix_human.pbs

@@ -22,7 +22,8 @@ AFACTOR=CTCF
 BFACTOR=POLR2H
 
 OUTPUT=results/mix_human/$DEPTH
-[ -d $OUTPUT ] || mkdir -p $OUTPUT
+[ -d results/mix_human ] || mkdir results/mix_human
+[ -d $OUTPUT ] || mkdir $OUTPUT
 
 MIX=../scripts/mix_fastq.sh
 ABASE=results/$REF/$DEPTH/$EPITOPE/$AFACTOR/FASTQ/Simulation_$PBS_ARRAYID

paper/SyntheticEpitope/job/run_mix_yeast.pbs

@@ -22,6 +22,7 @@ AFACTOR=Rap1
 BFACTOR=Reb1
 
 OUTPUT=results/mix_yeast/$DEPTH
+[ -d results/mix_yeast ] || mkdir results/mix_yeast ]
 [ -d $OUTPUT ] || mkdir -p $OUTPUT
 
 MIX=../scripts/mix_fastq.sh

paper/SyntheticEpitope/scripts/build_lineplots.py

@@ -108,9 +108,11 @@ def getParams():
 		fig.suptitle('Mix-Human')
 
 	# Set axis limits
+	# plt.xlim(10, 90)
+	# plt.xticks(range(10,91,10))
 	plt.xlim(0, 100)
-	plt.ylim(0, 1000)
 	plt.xticks(range(0,101,10))
+	plt.ylim(0, 1000)
 
 	# Save figure by output filename
 	# fig.savefig('results/blah.svg')

paper/scripts/mix_fastq.sh

@@ -93,4 +93,4 @@ seqtk subseq $BFQ\_R2.fastq.gz $OFQ\_readnames.txt >> $OFQ\_R2.fastq
 gzip -f $OFQ\_R1.fastq
 gzip -f $OFQ\_R2.fastq
 
-#rm $OFQ\_readnames.txt
+rm $OFQ\_readnames.txt