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  1. export PBTHOME=/home/arq5x/cphg-home/projects/pybedtools
  2.  
  3. shuffle 1094PC0012.bed > a.shuf.full.bed
  4. shuffle 1094PC0012.bed > b.shuf.full.bed
  5. head -1000 a.shuf.full.bed > a.shuf.1e3.bed; head -1000 b.shuf.full.bed > b.shuf.1e3.bed
  6. head -10000 a.shuf.full.bed > a.shuf.1e4.bed; head -10000 b.shuf.full.bed > b.shuf.1e4.bed
  7. head -100000 a.shuf.full.bed > a.shuf.1e5.bed; head -100000 b.shuf.full.bed > b.shuf.1e5.bed
  8. head -1000000 a.shuf.full.bed > a.shuf.1e6.bed; head -1000000 b.shuf.full.bed > b.shuf.1e6.bed
  9. head -10000000 a.shuf.full.bed > a.shuf.1e7.bed; head -10000000 b.shuf.full.bed > b.shuf.1e7.bed
  10. head -100000000 a.shuf.full.bed > a.shuf.1e8.bed; head -100000000 b.shuf.full.bed > b.shuf.1e8.bed
  11.  
  12. ###################################################
  13. # intersectBed full join (-wa, -wb)
  14. ###################################################
  15. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e3.bed -b b.shuf.1e3.bed -wa -wb > /dev/null" | \
  16. 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
  17. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e4.bed -b b.shuf.1e4.bed -wa -wb > /dev/null" | \
  18. 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
  19. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e5.bed -b b.shuf.1e5.bed -wa -wb > /dev/null" | \
  20. 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
  21. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e6.bed -b b.shuf.1e6.bed -wa -wb > /dev/null" | \
  22. 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
  23. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e7.bed -b b.shuf.1e7.bed -wa -wb > /dev/null" | \
  24. 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
  25. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e8.bed -b b.shuf.1e8.bed -wa -wb > /dev/null" | \
  26. 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
  27.  
  28. ###################################################
  29. # intersectBed full join (-u)
  30. ###################################################
  31. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e3.bed -b b.shuf.1e3.bed -u > /dev/null" | \
  32. 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
  33. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e4.bed -b b.shuf.1e4.bed -u > /dev/null" | \
  34. 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
  35. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e5.bed -b b.shuf.1e5.bed -u > /dev/null" | \
  36. 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
  37. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e6.bed -b b.shuf.1e6.bed -u > /dev/null" | \
  38. 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
  39. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e7.bed -b b.shuf.1e7.bed -u > /dev/null" | \
  40. 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
  41. echo "cd $PBTHOME; runit intersectBed -a a.shuf.1e8.bed -b b.shuf.1e8.bed -u > /dev/null" | \
  42. 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
  43.  
  44. ###################################################
  45. # bedIntersect full join* not really
  46. ###################################################
  47. echo "cd $PBTHOME; runit bedIntersect a.shuf.1e3.bed b.shuf.1e3.bed stdout > /dev/null" | \
  48. 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
  49. echo "cd $PBTHOME; runit bedIntersect a.shuf.1e4.bed b.shuf.1e4.bed stdout > /dev/null" | \
  50. 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
  51. echo "cd $PBTHOME; runit bedIntersect a.shuf.1e5.bed b.shuf.1e5.bed stdout > /dev/null" | \
  52. 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
  53. echo "cd $PBTHOME; runit bedIntersect a.shuf.1e6.bed b.shuf.1e6.bed stdout > /dev/null" | \
  54. 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
  55. echo "cd $PBTHOME; runit bedIntersect a.shuf.1e7.bed b.shuf.1e7.bed stdout > /dev/null" | \
  56. 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
  57. echo "cd $PBTHOME; runit bedIntersect a.shuf.1e8.bed b.shuf.1e8.bed stdout > /dev/null" | \
  58. 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
  59.  
  60. ###################################################
  61. # bedIntersect uniq
  62. ###################################################
  63. echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e3.bed b.shuf.1e3.bed stdout > /dev/null" | \
  64. 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
  65. echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e4.bed b.shuf.1e4.bed stdout > /dev/null" | \
  66. 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
  67. echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e5.bed b.shuf.1e5.bed stdout > /dev/null" | \
  68. 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
  69. echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e6.bed b.shuf.1e6.bed stdout > /dev/null" | \
  70. 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
  71. echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e7.bed b.shuf.1e7.bed stdout > /dev/null" | \
  72. 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
  73. echo "cd $PBTHOME; runit bedIntersect -aHitAny a.shuf.1e8.bed b.shuf.1e8.bed stdout > /dev/null" | \
  74. 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
  75.  
  76. ####################################################
  77. # pybedtools full
  78. ####################################################
  79. echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \
  80. 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
  81. echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \
  82. 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
  83. echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \
  84. 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
  85. echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \
  86. 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
  87. echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \
  88. 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
  89. echo "cd $PBTHOME; runit ./pybedtools-intersect-full.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \
  90. 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
  91.  
  92. ####################################################
  93. # pybedtools uniq
  94. ####################################################
  95. echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \
  96. 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
  97. echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \
  98. 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
  99. echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \
  100. 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
  101. echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \
  102. 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
  103. echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \
  104. 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
  105. echo "cd $PBTHOME; runit ./pybedtools-intersect-uniq.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \
  106. 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
  107.  
  108. ####################################################
  109. # bx-python full
  110. ####################################################
  111. echo "cd $PBTHOME; runit interval_join.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \
  112. 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
  113. echo "cd $PBTHOME; runit interval_join.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \
  114. 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
  115. echo "cd $PBTHOME; runit interval_join.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \
  116. 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
  117. echo "cd $PBTHOME; runit interval_join.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \
  118. 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
  119. echo "cd $PBTHOME; runit interval_join.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \
  120. 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
  121. echo "cd $PBTHOME; runit interval_join.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \
  122. 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
  123.  
  124.  
  125. ####################################################
  126. # bx-python uniq
  127. ####################################################
  128. echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e3.bed b.shuf.1e3.bed > /dev/null" | \
  129. 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
  130. echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e4.bed b.shuf.1e4.bed > /dev/null" | \
  131. 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
  132. echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e5.bed b.shuf.1e5.bed > /dev/null" | \
  133. 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
  134. echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e6.bed b.shuf.1e6.bed > /dev/null" | \
  135. 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
  136. echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e7.bed b.shuf.1e7.bed > /dev/null" | \
  137. 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
  138. echo "cd $PBTHOME; runit bed_intersect.py a.shuf.1e8.bed b.shuf.1e8.bed > /dev/null" | \
  139. 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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