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August 12, 2011 20:09
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pybedtools manuscript
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export PBTHOME=/home/arq5x/cphg-home/projects/pybedtools | |
shuffle 1094PC0012.bed > a.shuf.full.bed | |
shuffle 1094PC0012.bed > b.shuf.full.bed | |
head -1000 a.shuf.full.bed > a.shuf.1e3.bed; head -1000 b.shuf.full.bed > b.shuf.1e3.bed | |
head -10000 a.shuf.full.bed > a.shuf.1e4.bed; head -10000 b.shuf.full.bed > b.shuf.1e4.bed | |
head -100000 a.shuf.full.bed > a.shuf.1e5.bed; head -100000 b.shuf.full.bed > b.shuf.1e5.bed | |
head -1000000 a.shuf.full.bed > a.shuf.1e6.bed; head -1000000 b.shuf.full.bed > b.shuf.1e6.bed | |
head -10000000 a.shuf.full.bed > a.shuf.1e7.bed; head -10000000 b.shuf.full.bed > b.shuf.1e7.bed | |
head -100000000 a.shuf.full.bed > a.shuf.1e8.bed; head -100000000 b.shuf.full.bed > b.shuf.1e8.bed | |
################################################### | |
# intersectBed full join (-wa, -wb) | |
################################################### | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e3.bed -b b.shuf.1e3.bed -wa -wb > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e3-join | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e4.bed -b b.shuf.1e4.bed -wa -wb > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e4-join | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e5.bed -b b.shuf.1e5.bed -wa -wb > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e5-join | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e6.bed -b b.shuf.1e6.bed -wa -wb > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e6-join | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e7.bed -b b.shuf.1e7.bed -wa -wb > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e7-join | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e8.bed -b b.shuf.1e8.bed -wa -wb > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e8-join | |
################################################### | |
# intersectBed full join (-u) | |
################################################### | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e3.bed -b b.shuf.1e3.bed -u > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e3-uniq | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e4.bed -b b.shuf.1e4.bed -u > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e4-uniq | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e5.bed -b b.shuf.1e5.bed -u > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e5-uniq | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e6.bed -b b.shuf.1e6.bed -u > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e6-uniq | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e7.bed -b b.shuf.1e7.bed -u > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e7-uniq | |
echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e8.bed -b b.shuf.1e8.bed -u > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bt-e8-uniq | |
################################################### | |
# bedIntersect full join* not really | |
################################################### | |
echo "cd $PBTHOME; runit bedIntersect a.shuf.1e3.bed b.shuf.1e3.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e3-join | |
echo "cd $PBTHOME; runit bedIntersect a.shuf.1e4.bed b.shuf.1e4.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e4-join | |
echo "cd $PBTHOME; runit bedIntersect a.shuf.1e5.bed b.shuf.1e5.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e5-join | |
echo "cd $PBTHOME; runit bedIntersect a.shuf.1e6.bed b.shuf.1e6.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e6-join | |
echo "cd $PBTHOME; runit bedIntersect a.shuf.1e7.bed b.shuf.1e7.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e7-join | |
echo "cd $PBTHOME; runit bedIntersect a.shuf.1e8.bed b.shuf.1e8.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e8-join | |
################################################### | |
# bedIntersect uniq | |
################################################### | |
echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e3.bed b.shuf.1e3.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e3-uniq | |
echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e4.bed b.shuf.1e4.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e4-uniq | |
echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e5.bed b.shuf.1e5.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e5-uniq | |
echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e6.bed b.shuf.1e6.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e6-uniq | |
echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e7.bed b.shuf.1e7.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e7-uniq | |
echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e8.bed b.shuf.1e8.bed stdout > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N kent-e8-uniq | |
#################################################### | |
# pybedtools full | |
#################################################### | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e3-full | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e4-full | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e5-full | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e6-full | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e7-full | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e8-full | |
#################################################### | |
# pybedtools uniq | |
#################################################### | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e3-uniq | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e4-uniq | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e5-uniq | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e6-uniq | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e7-uniq | |
echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N pbt-e8-uniq | |
#################################################### | |
# bx-python full | |
#################################################### | |
echo "cd $PBTHOME; runit interval_join.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e3-full | |
echo "cd $PBTHOME; runit interval_join.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e4-full | |
echo "cd $PBTHOME; runit interval_join.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e5-full | |
echo "cd $PBTHOME; runit interval_join.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e6-full | |
echo "cd $PBTHOME; runit interval_join.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e7-full | |
echo "cd $PBTHOME; runit interval_join.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=90000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e8-full | |
#################################################### | |
# bx-python uniq | |
#################################################### | |
echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e3-uniq | |
echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e4-uniq | |
echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e5-uniq | |
echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e6-uniq | |
echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=64000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e7-uniq | |
echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \ | |
qsub -q cphg -W group_list=CPHG -V -l select=1:mem=90000m:ncpus=1 -m bea -M arq5x@virginia.edu -N bx-e8-uniq |
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