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In [1]:

    
%matplotlib inline



In [2]:

    
import glob
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib
pd.set_option('display.max_columns', 50) # print all rows


import os
os.chdir('/Users/evanbiederstedt/Downloads/RRBS_data_files')

import statsmodels.api as sm



In [3]:

    
"""
Normal_B_regions.csv
pcell_regions.csv
trito_regions.csv
mcell_regions.csv
CD19cell_regions.csv
cw154_regions.csv
"""









    Out[3]:





'\nNormal_B_regions.csv\npcell_regions.csv\ntrito_regions.csv\nmcell_regions.csv\nCD19cell_regions.csv\ncw154_regions.csv\n'



In [6]:

    
normalB = pd.read_csv("Normal_B_regions.csv")
mcell = pd.read_csv("mcell_regions.csv")
pcell = pd.read_csv("pcell_regions.csv")
cd19cell = pd.read_csv("CD19cell_regions.csv")
trito = pd.read_csv("trito_regions.csv")
cw154 = pd.read_csv("cw154_regions.csv")



In [9]:

    
print(normalB.shape)
print(mcell.shape)
print(pcell.shape)
print(cd19cell.shape)
print(trito.shape)
print(cw154.shape)









    



(136, 39)
(88, 39)
(90, 39)
(89, 39)
(44, 39)
(66, 39)



In [10]:

    
136 + 88 + 90 + 89









    Out[10]:





403



In [11]:

    
44 + 66









    Out[11]:





110



In [37]:

    
# there are 104 CLL
# there are 342 normal 
#
# 113 normal B



In [38]:

    
"""
# remove 6 CLL cells

3	RRBS_trito_pool_1_TAAGGCGA.AGGATG.dan.anno
43	RRBS_trito_pool_2_CGTACTAG.TGCTGC.dan.anno
11	RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CTAT..
18	RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GTTG...
29	RRBS_cw154_Tris_protease_CTCTCTAC.CAAGAG.dan.anno
51	RRBS_cw154_Tris_protease_GR_CAGAGAGG.CAAGAG.da..
"""









    Out[38]:





'\n3\tRRBS_trito_pool_1_TAAGGCGA.AGGATG.dan.anno\n43\tRRBS_trito_pool_2_CGTACTAG.TGCTGC.dan.anno\n11\tRRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CTAT..\n18\tRRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GTTG...\n29\tRRBS_cw154_Tris_protease_CTCTCTAC.CAAGAG.dan.anno\n51\tRRBS_cw154_Tris_protease_GR_CAGAGAGG.CAAGAG.da..\n'



In [42]:

    
print(normalB.shape)
print(mcell.shape)
print(pcell.shape)
print(cd19cell.shape)









    



(136, 39)
(88, 39)
(90, 39)
(89, 39)



In [43]:

    
# 84 total cd19cell; should be 5 cut









    Out[43]:





83



In [44]:

    
# 70 total pcell; should be 20









    Out[44]:





69



In [45]:

    
# 75 total mcell; should be 13 cut









    Out[45]:





74



In [46]:

    
# 113 total normal B; should cut 23



In [82]:

    
84+70+75+113









    Out[82]:





342



In [83]:

    
136-24









    Out[83]:





112



In [84]:

    
"""
# remove 20 pcell
2	RRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.ACGTGG..
13	RRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.GACACG
20	RRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.TATCTC...
21	RRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.TCTCTG..
44	RRBS_NormalBCD19pCD27pcell23_44_CTCTCTAC.TGCTG
45	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.ACAAC...
47	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.ACGTG
49	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.AGGAT..
51	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.ATCGA.
53	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.CATGA
55	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.CGGTA.
57	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.CTCAG.
59	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GCATT...
60	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GCTGC
61	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GGCAT.
63	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GTTGA
65	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.TATCT..
66	RRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.TCTCT...
74	RRBS_NormalBCD19pCD27pcell67_88_GCTACGCT.CAAGA
89	RRBS_NormalBCD19pCD27pcell67_88_GCTACGCT.TGCTG.

# remove 23 normal B cell
3	RRBS_normal_B_cell_A1_24_TAAGGCGA.ACTCAC.dan.anno
9	RRBS_normal_B_cell_A1_24_TAAGGCGA.CCTTCG.dan.anno
14	RRBS_normal_B_cell_A1_24_TAAGGCGA.GCATTC.dan.anno
23	RRBS_normal_B_cell_A1_24_TAAGGCGA.TGCTGC.dan.anno
26	RRBS_normal_B_cell_B1_24_CGTACTAG.ACGTGG.dan.anno
28	RRBS_normal_B_cell_B1_24_CGTACTAG.AGGATG.dan.anno
30	RRBS_normal_B_cell_B1_24_CGTACTAG.ATCGAC.dan.anno
39	RRBS_normal_B_cell_B1_24_CGTACTAG.GCTGCC.dan.anno
57	RRBS_normal_B_cell_C1_24_AGGCAGAA.CCTTCG.dan.anno
60	RRBS_normal_B_cell_C1_24_AGGCAGAA.CTCAGC.dan.anno
69	RRBS_normal_B_cell_C1_24_AGGCAGAA.TCTCTG.dan.anno
75	RRBS_normal_B_cell_D1_24_TCCTGAGC.ATAGCG.dan.anno
79	RRBS_normal_B_cell_D1_24_TCCTGAGC.CCTTCG.dan.anno
82	RRBS_normal_B_cell_D1_24_TCCTGAGC.CTCAGC.dan.anno
87	RRBS_normal_B_cell_D1_24_TCCTGAGC.GTGAGG.dan.anno
91	RRBS_normal_B_cell_D1_24_TCCTGAGC.TCTCTG.dan.anno
97	RRBS_normal_B_cell_G1_22_GGACTCCT.ATAGCG.dan.anno
109	RRBS_normal_B_cell_G1_22_GGACTCCT.GTGAGG.dan.anno
113	RRBS_normal_B_cell_G1_22_GGACTCCT.TCTCTG.dan.anno
123	RRBS_normal_B_cell_H1_22_TAGGCATG.CCTTCG.dan.anno
128	RRBS_normal_B_cell_H1_22_TAGGCATG.GCATTC.dan.anno
132	RRBS_normal_B_cell_H1_22_TAGGCATG.GTTGAG.dan.anno
135	RRBS_normal_B_cell_H1_22_TAGGCATG.TCTCTG.dan.anno


# remove 13 mcell
0	RRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.ACAACC.
4	RRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.AGGATG
10	RRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.CGGTAG..
21	RRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.TCTCTG...
37	RRBS_NormalBCD19pCD27mcell23_44_GTAGAGGA.GCTGC.
38	RRBS_NormalBCD19pCD27mcell23_44_GTAGAGGA.GGCAT
41	RRBS_NormalBCD19pCD27mcell23_44_GTAGAGGA.TAGCG..
45	RRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.ACCGC.
58	RRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GCATT...
59	RRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GCTGC
60	RRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GGCAT.
62	RRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GTTGA.
81	RRBS_NormalBCD19pCD27mcell67_88_CGTACTAG.GCTGC


# remove 5 cd19 cell
17	RRBS_NormalBCD19pcell1_22_TAAGGCGA.GTGAGG.dan...
29	RRBS_NormalBCD19pcell23_44_CGTACTAG.CAAGAG.dan.
40	RRBS_NormalBCD19pcell23_44_CGTACTAG.GTTGAG.dan...
79	RRBS_NormalBCD19pcell67_88_TCCTGAGC.GACACG.dan..
88	RRBS_NormalBCD19pcell67_88_TCCTGAGC.TGCTGC.dan




"""









    Out[84]:





'\n# remove 20 pcell\n2\tRRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.ACGTGG..\n13\tRRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.GACACG\n20\tRRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.TATCTC...\n21\tRRBS_NormalBCD19pCD27pcell1_22_TAGGCATG.TCTCTG..\n44\tRRBS_NormalBCD19pCD27pcell23_44_CTCTCTAC.TGCTG\n45\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.ACAAC...\n47\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.ACGTG\n49\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.AGGAT..\n51\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.ATCGA.\n53\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.CATGA\n55\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.CGGTA.\n57\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.CTCAG.\n59\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GCATT...\n60\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GCTGC\n61\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GGCAT.\n63\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.GTTGA\n65\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.TATCT..\n66\tRRBS_NormalBCD19pCD27pcell45_66_CAGAGAGG.TCTCT...\n74\tRRBS_NormalBCD19pCD27pcell67_88_GCTACGCT.CAAGA\n89\tRRBS_NormalBCD19pCD27pcell67_88_GCTACGCT.TGCTG.\n\n# remove 23 normal B cell\n3\tRRBS_normal_B_cell_A1_24_TAAGGCGA.ACTCAC.dan.anno\n9\tRRBS_normal_B_cell_A1_24_TAAGGCGA.CCTTCG.dan.anno\n14\tRRBS_normal_B_cell_A1_24_TAAGGCGA.GCATTC.dan.anno\n23\tRRBS_normal_B_cell_A1_24_TAAGGCGA.TGCTGC.dan.anno\n26\tRRBS_normal_B_cell_B1_24_CGTACTAG.ACGTGG.dan.anno\n28\tRRBS_normal_B_cell_B1_24_CGTACTAG.AGGATG.dan.anno\n30\tRRBS_normal_B_cell_B1_24_CGTACTAG.ATCGAC.dan.anno\n39\tRRBS_normal_B_cell_B1_24_CGTACTAG.GCTGCC.dan.anno\n57\tRRBS_normal_B_cell_C1_24_AGGCAGAA.CCTTCG.dan.anno\n60\tRRBS_normal_B_cell_C1_24_AGGCAGAA.CTCAGC.dan.anno\n69\tRRBS_normal_B_cell_C1_24_AGGCAGAA.TCTCTG.dan.anno\n75\tRRBS_normal_B_cell_D1_24_TCCTGAGC.ATAGCG.dan.anno\n79\tRRBS_normal_B_cell_D1_24_TCCTGAGC.CCTTCG.dan.anno\n82\tRRBS_normal_B_cell_D1_24_TCCTGAGC.CTCAGC.dan.anno\n87\tRRBS_normal_B_cell_D1_24_TCCTGAGC.GTGAGG.dan.anno\n91\tRRBS_normal_B_cell_D1_24_TCCTGAGC.TCTCTG.dan.anno\n97\tRRBS_normal_B_cell_G1_22_GGACTCCT.ATAGCG.dan.anno\n109\tRRBS_normal_B_cell_G1_22_GGACTCCT.GTGAGG.dan.anno\n113\tRRBS_normal_B_cell_G1_22_GGACTCCT.TCTCTG.dan.anno\n123\tRRBS_normal_B_cell_H1_22_TAGGCATG.CCTTCG.dan.anno\n128\tRRBS_normal_B_cell_H1_22_TAGGCATG.GCATTC.dan.anno\n132\tRRBS_normal_B_cell_H1_22_TAGGCATG.GTTGAG.dan.anno\n135\tRRBS_normal_B_cell_H1_22_TAGGCATG.TCTCTG.dan.anno\n\n\n# remove 13 mcell\n0\tRRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.ACAACC.\n4\tRRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.AGGATG\n10\tRRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.CGGTAG..\n21\tRRBS_NormalBCD19pCD27mcell1_22_CGAGGCTG.TCTCTG...\n37\tRRBS_NormalBCD19pCD27mcell23_44_GTAGAGGA.GCTGC.\n38\tRRBS_NormalBCD19pCD27mcell23_44_GTAGAGGA.GGCAT\n41\tRRBS_NormalBCD19pCD27mcell23_44_GTAGAGGA.TAGCG..\n45\tRRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.ACCGC.\n58\tRRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GCATT...\n59\tRRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GCTGC\n60\tRRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GGCAT.\n62\tRRBS_NormalBCD19pCD27mcell45_66_TAAGGCGA.GTTGA.\n81\tRRBS_NormalBCD19pCD27mcell67_88_CGTACTAG.GCTGC\n\n\n# remove 5 cd19 cell\n17\tRRBS_NormalBCD19pcell1_22_TAAGGCGA.GTGAGG.dan...\n29\tRRBS_NormalBCD19pcell23_44_CGTACTAG.CAAGAG.dan.\n40\tRRBS_NormalBCD19pcell23_44_CGTACTAG.GTTGAG.dan...\n79\tRRBS_NormalBCD19pcell67_88_TCCTGAGC.GACACG.dan..\n88\tRRBS_NormalBCD19pcell67_88_TCCTGAGC.TGCTGC.dan\n\n\n\n\n'



In [ ]:

    
normalB = normalB.drop(normalB.index[])



In [ ]:

    
normalB.index[]



In [89]:

    
# remove 23 normal B cell
normalB = normalB.drop(normalB.index[[3,9,14,23,26,28,30,39,57,60,69,75,79,82,87,91,97,109,113,123,128,132,135]])



In [88]:

    
len([3,9,14,23,26,28,30,39,57,60,69,75,79,82,87,91,97,109,113,123,128,132,135])









    Out[88]:





23



In [91]:

    
normalB = normalB.reset_index()



In [92]:

    
normalB.shape









    Out[92]:





(113, 40)



In [93]:

    
normalB.to_csv("Correct_Normal_B_regions.csv", index=False)



In [95]:

    
len([2,13,20,21,44,45,47,49,51,53,55,57,59,60,61,63,65,66,74,89])









    Out[95]:





20



In [96]:

    
pcell = pcell.drop(pcell.index[[2,13,20,21,44,45,47,49,51,53,55,57,59,60,61,63,65,66,74,89]])



In [97]:

    
pcell = pcell.reset_index()



In [98]:

    
pcell.shape









    Out[98]:





(70, 40)



In [99]:

    
pcell.to_csv("Correct_pcell_regions.csv", index=False)



In [101]:

    
len([0,4,10,21,37,38,41,45,58,59,60,62,81])









    Out[101]:





13



In [102]:

    
mcell = mcell.drop(mcell.index[[0,4,10,21,37,38,41,45,58,59,60,62,81]])



In [103]:

    
mcell = mcell.reset_index()



In [104]:

    
mcell.shape









    Out[104]:





(75, 40)



In [105]:

    
mcell.to_csv("Correct_mcell_regions.csv", index=False)



In [106]:

    
len([17, 29, 40, 79, 88])









    Out[106]:





5



In [107]:

    
cd19cell = cd19cell.drop(cd19cell.index[[17, 29, 40, 79, 88]])



In [108]:

    
cd19cell = cd19cell.reset_index()



In [109]:

    
cd19cell.shape









    Out[109]:





(84, 40)



In [110]:

    
cd19cell.to_csv("Correct_CD19cell_regions.csv", index=False)



In [112]:

    
trito = trito.drop(trito.index[[3, 43]])



In [113]:

    
trito = trito.reset_index()



In [114]:

    
trito.shape









    Out[114]:





(42, 40)



In [115]:

    
trito.to_csv("Correct_trito_regions.csv", index=False)



In [116]:

    
cw154









    Out[116]:






  
    
      
      filename
      methylation_tssDistance
      methylation_genesDistance
      methylation_exonsDistance
      methylation_intronsDistance
      methylation_promoterDistance
      methylation_cgiDistance
      methylation_ctcfDistance
      methylation_ctcfUpDistance
      methylation_ctcfDownDistance
      methylation_geneDistalRegulatoryModulesDistance
      methylation_vistaEnhancersDistance
      methylation_3PrimeUTRDistance
      methylation_5PrimeUTRDistance
      methylation_firstExonDistance
      methylation_geneDistalRegulatoryModulesK562Distance
      methylation_hypoInHues64Distance
      methylation_intergenic
      methylation_shore
      methylation_shelf
      PDR_tssDistance
      PDR_genesDistance
      PDR_exonsDistance
      PDR_intronsDistance
      PDR_promoterDistance
      PDR_cgiDistance
      PDR_ctcfDistance
      PDR_ctcfUpDistance
      PDR_ctcfDownDistance
      PDR_geneDistalRegulatoryModulesDistance
      PDR_vistaEnhancersDistance
      PDR_3PrimeUTRDistance
      PDR_5PrimeUTRDistance
      PDR_firstExonDistance
      PDR_geneDistalRegulatoryModulesK562Distance
      PDR_hypoInHues64Distance
      PDR_intergenic
      PDR_shore
      PDR_shelf
    
  
  
    
      0
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.ACAA...
      0.0
      0.557445
      0.387638
      0.583685
      0.148984
      0.173551
      0.197546
      0.0
      0.197546
      0.330378
      0.534917
      0.659609
      0.300969
      0.142909
      0.246735
      0.805699
      0.820512
      0.590658
      0.806973
      0.0
      0.370149
      0.420504
      0.359511
      0.408136
      0.450911
      0.436709
      0.0
      0.436709
      0.446102
      0.393463
      0.409348
      0.376109
      0.438725
      0.388377
      0.397393
      0.379858
      0.378600
      0.345222
    
    
      1
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.ACCG...
      0.0
      0.495537
      0.324467
      0.521993
      0.140566
      0.157658
      0.175575
      0.0
      0.175575
      0.296219
      0.366917
      0.587535
      0.261936
      0.137202
      0.237040
      0.690698
      0.796567
      0.530634
      0.780923
      0.0
      0.388093
      0.435418
      0.383256
      0.418755
      0.458484
      0.442186
      0.0
      0.442186
      0.440632
      0.840602
      0.376294
      0.386659
      0.445932
      0.394716
      0.346512
      0.418598
      0.404386
      0.362456
    
    
      2
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.ACGT...
      0.0
      0.520409
      0.357209
      0.544602
      0.138190
      0.161856
      0.202110
      0.0
      0.202110
      0.314849
      0.463004
      0.656101
      0.275719
      0.138640
      0.225783
      0.761359
      0.792970
      0.551861
      0.785731
      0.0
      0.383971
      0.430167
      0.374988
      0.410647
      0.455464
      0.453277
      0.0
      0.453277
      0.450694
      0.324865
      0.443011
      0.387172
      0.439933
      0.414011
      0.280260
      0.411414
      0.389000
      0.363575
    
    
      3
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.ACTC...
      0.0
      0.569906
      0.398614
      0.595372
      0.158028
      0.178889
      0.196911
      0.0
      0.196911
      0.340942
      0.608100
      0.665446
      0.310607
      0.154927
      0.247978
      0.867355
      0.831256
      0.609382
      0.812445
      0.0
      0.363173
      0.416487
      0.354378
      0.421272
      0.454977
      0.438265
      0.0
      0.438265
      0.452257
      0.477332
      0.376957
      0.382624
      0.449764
      0.400321
      0.171406
      0.369736
      0.385435
      0.345905
    
    
      4
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.AGGA...
      0.0
      0.554293
      0.390193
      0.576205
      0.148946
      0.173784
      0.194668
      0.0
      0.194668
      0.339245
      0.494894
      0.652036
      0.291318
      0.145185
      0.250083
      0.894932
      0.825017
      0.592558
      0.807747
      0.0
      0.365658
      0.414198
      0.357211
      0.407138
      0.447926
      0.433596
      0.0
      0.433596
      0.428716
      0.406863
      0.397655
      0.376272
      0.425466
      0.383864
      0.274772
      0.382212
      0.378352
      0.346732
    
    
      5
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.ATAG...
      0.0
      0.526884
      0.365643
      0.552338
      0.136827
      0.156219
      0.186982
      0.0
      0.186982
      0.301051
      0.415511
      0.644089
      0.271955
      0.138062
      0.216288
      0.857859
      0.811758
      0.577252
      0.782210
      0.0
      0.367963
      0.412391
      0.359439
      0.403460
      0.439426
      0.423300
      0.0
      0.423300
      0.429729
      0.292245
      0.380568
      0.375672
      0.428114
      0.370678
      0.322551
      0.389826
      0.380924
      0.350955
    
    
      6
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.ATCG...
      0.0
      0.565536
      0.398508
      0.589354
      0.153438
      0.180336
      0.206914
      0.0
      0.206914
      0.347903
      0.522757
      0.669365
      0.309018
      0.148969
      0.258009
      0.820103
      0.819525
      0.596228
      0.804310
      0.0
      0.369158
      0.418102
      0.361217
      0.417424
      0.458302
      0.448756
      0.0
      0.448756
      0.443698
      0.440532
      0.368417
      0.382661
      0.443897
      0.395646
      0.354083
      0.387312
      0.389256
      0.340801
    
    
      7
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CAAG...
      0.0
      0.547472
      0.384373
      0.572749
      0.152863
      0.174421
      0.196066
      0.0
      0.196066
      0.323417
      0.597436
      0.672153
      0.293574
      0.158459
      0.240607
      0.824585
      0.818860
      0.588054
      0.798634
      0.0
      0.376000
      0.434308
      0.366559
      0.423294
      0.459171
      0.451662
      0.0
      0.451662
      0.447380
      0.488112
      0.390544
      0.391449
      0.454109
      0.397710
      0.296812
      0.377959
      0.384896
      0.350755
    
    
      8
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CATG...
      0.0
      0.560115
      0.399275
      0.582994
      0.152070
      0.177982
      0.210642
      0.0
      0.210642
      0.340830
      0.435017
      0.658850
      0.302575
      0.158123
      0.251308
      0.843652
      0.824098
      0.590612
      0.803914
      0.0
      0.373358
      0.424900
      0.366055
      0.417887
      0.459681
      0.468793
      0.0
      0.468793
      0.450033
      0.352024
      0.396828
      0.387961
      0.445253
      0.403604
      0.319329
      0.384551
      0.390295
      0.359863
    
    
      9
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CCTT...
      0.0
      0.532219
      0.373563
      0.554328
      0.142907
      0.169012
      0.183736
      0.0
      0.183736
      0.302616
      0.550507
      0.615149
      0.286602
      0.137620
      0.221478
      0.836297
      0.797139
      0.569496
      0.783430
      0.0
      0.385187
      0.431739
      0.377812
      0.418669
      0.460034
      0.465381
      0.0
      0.465381
      0.453603
      0.594966
      0.418134
      0.380153
      0.439284
      0.396606
      0.339958
      0.408284
      0.396687
      0.369618
    
    
      10
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CGGT...
      0.0
      0.531700
      0.370532
      0.555725
      0.143834
      0.165315
      0.196658
      0.0
      0.196658
      0.309425
      0.623132
      0.622519
      0.289789
      0.155198
      0.227672
      0.843004
      0.805881
      0.560993
      0.780727
      0.0
      0.382102
      0.430692
      0.375433
      0.424467
      0.459925
      0.446492
      0.0
      0.446492
      0.438186
      0.285556
      0.395191
      0.396617
      0.457859
      0.385372
      0.288365
      0.385553
      0.395152
      0.348968
    
    
      11
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CTAT...
      0.0
      0.000000
      0.438795
      0.584559
      0.167596
      0.132262
      0.247382
      0.0
      0.247382
      0.367269
      0.666667
      0.802508
      0.266462
      0.184211
      0.438384
      NaN
      0.864040
      0.753557
      0.898721
      0.0
      0.320416
      0.364490
      0.306668
      0.356688
      0.364810
      0.492147
      0.0
      0.492147
      0.336617
      1.000000
      0.278997
      0.367534
      0.408669
      0.282828
      0.000000
      0.255152
      0.306773
      0.166311
    
    
      12
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.CTCA...
      0.0
      0.541012
      0.377389
      0.563507
      0.145227
      0.168764
      0.192585
      0.0
      0.192585
      0.316389
      0.499417
      0.620360
      0.294856
      0.143099
      0.234895
      0.807127
      0.815787
      0.578767
      0.792081
      0.0
      0.376073
      0.421432
      0.367262
      0.419961
      0.462968
      0.441023
      0.0
      0.441023
      0.437581
      0.588098
      0.388470
      0.389301
      0.439037
      0.393979
      0.358086
      0.389474
      0.390579
      0.352459
    
    
      13
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GACA...
      0.0
      0.539446
      0.379285
      0.562106
      0.151057
      0.169830
      0.197479
      0.0
      0.197479
      0.319023
      0.526829
      0.624394
      0.298679
      0.152752
      0.245067
      0.817265
      0.808146
      0.560909
      0.785910
      0.0
      0.383113
      0.442335
      0.372629
      0.432990
      0.474104
      0.484110
      0.0
      0.484110
      0.456716
      0.394038
      0.435484
      0.392065
      0.465344
      0.397636
      0.453005
      0.394112
      0.399016
      0.354612
    
    
      14
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GCAT...
      0.0
      0.573906
      0.406627
      0.598475
      0.155752
      0.181375
      0.219125
      0.0
      0.219125
      0.349142
      0.461636
      0.692945
      0.314043
      0.149229
      0.265561
      0.805184
      0.818499
      0.600889
      0.805211
      0.0
      0.364838
      0.413731
      0.355293
      0.418106
      0.451039
      0.460955
      0.0
      0.460955
      0.439120
      0.427394
      0.374650
      0.384259
      0.436755
      0.386565
      0.237381
      0.388799
      0.388247
      0.351250
    
    
      15
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GCTG...
      0.0
      0.539193
      0.372853
      0.564383
      0.150046
      0.168813
      0.200850
      0.0
      0.200850
      0.317655
      0.268741
      0.630294
      0.293949
      0.147488
      0.230698
      0.821040
      0.793269
      0.565109
      0.775614
      0.0
      0.393342
      0.452026
      0.385192
      0.444778
      0.484272
      0.488233
      0.0
      0.488233
      0.459993
      0.214993
      0.453466
      0.409531
      0.469308
      0.402897
      0.556227
      0.403487
      0.399105
      0.359500
    
    
      16
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GGCA...
      0.0
      0.548961
      0.381545
      0.572243
      0.146518
      0.163592
      0.183910
      0.0
      0.183910
      0.332055
      0.649764
      0.659449
      0.302050
      0.137127
      0.242075
      0.858011
      0.802843
      0.573498
      0.788575
      0.0
      0.369289
      0.415335
      0.362727
      0.408150
      0.450432
      0.434240
      0.0
      0.434240
      0.448769
      0.330582
      0.427089
      0.369247
      0.423437
      0.403369
      0.205525
      0.403571
      0.402985
      0.363866
    
    
      17
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GTGA...
      0.0
      0.517231
      0.360581
      0.541139
      0.144744
      0.169206
      0.192751
      0.0
      0.192751
      0.305701
      0.480723
      0.644707
      0.272439
      0.143972
      0.224896
      0.918484
      0.809293
      0.549385
      0.774150
      0.0
      0.384798
      0.440085
      0.375126
      0.427821
      0.470287
      0.458102
      0.0
      0.458102
      0.450411
      0.491777
      0.418309
      0.398621
      0.454455
      0.393129
      0.153117
      0.377603
      0.389681
      0.372192
    
    
      18
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.GTTG...
      0.0
      0.445185
      0.314814
      0.459320
      0.101895
      0.106513
      0.175696
      0.0
      0.175696
      0.255117
      0.000000
      0.678481
      0.205315
      0.121112
      0.152685
      1.000000
      0.864037
      0.541609
      0.803819
      0.0
      0.289698
      0.302033
      0.274471
      0.305291
      0.323511
      0.320269
      0.0
      0.320269
      0.332025
      0.000000
      0.272405
      0.287926
      0.304364
      0.244743
      0.000000
      0.259456
      0.350199
      0.261936
    
    
      19
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.TAGC...
      0.0
      0.515064
      0.355504
      0.538392
      0.136692
      0.160634
      0.179352
      0.0
      0.179352
      0.304709
      0.444590
      0.584831
      0.275469
      0.136273
      0.232486
      0.726700
      0.784468
      0.534703
      0.769952
      0.0
      0.396907
      0.440482
      0.389549
      0.423470
      0.462821
      0.449771
      0.0
      0.449771
      0.465285
      0.426702
      0.407070
      0.397690
      0.445997
      0.414601
      0.361041
      0.422636
      0.409871
      0.372959
    
    
      20
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.TATC...
      0.0
      0.576698
      0.407457
      0.601190
      0.156286
      0.179898
      0.203588
      0.0
      0.203588
      0.341264
      0.581638
      0.672314
      0.322060
      0.151705
      0.253217
      0.870145
      0.827566
      0.609707
      0.808661
      0.0
      0.363719
      0.416227
      0.355604
      0.418422
      0.454966
      0.438377
      0.0
      0.438377
      0.442940
      0.321610
      0.394777
      0.380926
      0.444623
      0.400264
      0.253117
      0.374934
      0.378514
      0.347429
    
    
      21
      RRBS_cw154_CutSmart_proteinase_K_TAGGCATG.TCTC...
      0.0
      0.565269
      0.398589
      0.589572
      0.157359
      0.178807
      0.211161
      0.0
      0.211161
      0.342742
      0.563872
      0.681485
      0.312209
      0.155151
      0.256075
      0.863981
      0.828704
      0.602805
      0.808628
      0.0
      0.368633
      0.420777
      0.360477
      0.423342
      0.463158
      0.464180
      0.0
      0.464180
      0.449781
      0.310764
      0.373593
      0.395798
      0.454929
      0.396916
      0.177725
      0.372295
      0.384154
      0.345767
    
    
      22
      RRBS_cw154_Tris_protease_CTCTCTAC.ACAACC.dan.anno
      0.0
      0.534341
      0.373414
      0.559693
      0.140429
      0.159554
      0.178100
      0.0
      0.178100
      0.309936
      0.497813
      0.645147
      0.292520
      0.143238
      0.226691
      0.731040
      0.808980
      0.580810
      0.795186
      0.0
      0.388448
      0.444272
      0.377688
      0.433265
      0.469909
      0.469338
      0.0
      0.469338
      0.451973
      0.651118
      0.429110
      0.404743
      0.471306
      0.398084
      0.377739
      0.394894
      0.395843
      0.368690
    
    
      23
      RRBS_cw154_Tris_protease_CTCTCTAC.ACCGCG.dan.anno
      0.0
      0.460252
      0.301662
      0.485655
      0.123422
      0.144838
      0.161997
      0.0
      0.161997
      0.258069
      0.137171
      0.607551
      0.216179
      0.125607
      0.192525
      0.893236
      0.784792
      0.496794
      0.751479
      0.0
      0.393472
      0.439482
      0.385331
      0.422044
      0.459844
      0.438432
      0.0
      0.438432
      0.456989
      0.173419
      0.457588
      0.402154
      0.453262
      0.412374
      0.324368
      0.422718
      0.423725
      0.343020
    
    
      24
      RRBS_cw154_Tris_protease_CTCTCTAC.ACGTGG.dan.anno
      0.0
      0.458037
      0.323757
      0.482683
      0.127488
      0.161868
      0.176395
      0.0
      0.176395
      0.285677
      0.407810
      0.584367
      0.216456
      0.126353
      0.201637
      0.975253
      0.791770
      0.517245
      0.752050
      0.0
      0.410130
      0.440868
      0.407166
      0.426673
      0.464655
      0.448130
      0.0
      0.448130
      0.451854
      0.296589
      0.413079
      0.408591
      0.454207
      0.418433
      0.066367
      0.399408
      0.404818
      0.339397
    
    
      25
      RRBS_cw154_Tris_protease_CTCTCTAC.ACTCAC.dan.anno
      0.0
      0.590028
      0.422366
      0.612746
      0.168838
      0.192126
      0.204903
      0.0
      0.204903
      0.371221
      0.733536
      0.676370
      0.340330
      0.165456
      0.282602
      0.831377
      0.816232
      0.594412
      0.805338
      0.0
      0.381890
      0.444354
      0.372424
      0.453939
      0.496793
      0.476430
      0.0
      0.476430
      0.467415
      0.134052
      0.405989
      0.397287
      0.473730
      0.425922
      0.237761
      0.393858
      0.396729
      0.348192
    
    
      26
      RRBS_cw154_Tris_protease_CTCTCTAC.AGGATG.dan.anno
      0.0
      0.526552
      0.369634
      0.553452
      0.143346
      0.165112
      0.189923
      0.0
      0.189923
      0.319121
      0.419560
      0.650610
      0.281031
      0.137878
      0.234273
      0.826387
      0.793863
      0.560189
      0.785121
      0.0
      0.389957
      0.447900
      0.378239
      0.447429
      0.480496
      0.498393
      0.0
      0.498393
      0.459329
      0.192210
      0.399631
      0.408654
      0.479657
      0.409307
      0.294912
      0.419935
      0.403721
      0.382693
    
    
      27
      RRBS_cw154_Tris_protease_CTCTCTAC.ATAGCG.dan.anno
      0.0
      0.514725
      0.364374
      0.536571
      0.138552
      0.163622
      0.209144
      0.0
      0.209144
      0.301816
      0.432663
      0.641328
      0.275702
      0.138910
      0.225859
      0.926267
      0.798583
      0.542398
      0.777647
      0.0
      0.387464
      0.435454
      0.380125
      0.440076
      0.477478
      0.453723
      0.0
      0.453723
      0.448844
      0.455532
      0.378974
      0.401406
      0.462439
      0.404434
      0.175444
      0.404892
      0.414161
      0.349822
    
    
      28
      RRBS_cw154_Tris_protease_CTCTCTAC.ATCGAC.dan.anno
      0.0
      0.558080
      0.398185
      0.580534
      0.151438
      0.175596
      0.197664
      0.0
      0.197664
      0.334314
      0.433680
      0.703718
      0.302549
      0.152055
      0.248275
      0.877315
      0.819819
      0.581308
      0.796077
      0.0
      0.380517
      0.431675
      0.373339
      0.438100
      0.476924
      0.467834
      0.0
      0.467834
      0.464795
      0.732005
      0.401747
      0.402183
      0.468532
      0.413423
      0.445849
      0.379814
      0.380670
      0.343064
    
    
      29
      RRBS_cw154_Tris_protease_CTCTCTAC.CAAGAG.dan.anno
      0.0
      0.486270
      0.370296
      0.502550
      0.152896
      0.168602
      0.205128
      0.0
      0.205128
      0.170190
      0.235294
      0.743697
      0.231379
      0.191316
      0.100649
      0.500000
      0.848130
      0.564462
      0.827768
      0.0
      0.427703
      0.430160
      0.436737
      0.494695
      0.470844
      0.458974
      0.0
      0.458974
      0.465425
      1.000000
      0.340336
      0.543755
      0.458727
      0.457792
      0.000000
      0.335998
      0.348029
      0.298770
    
    
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    
    
      36
      RRBS_cw154_Tris_protease_CTCTCTAC.GCATTC.dan.anno
      0.0
      0.550686
      0.397458
      0.573475
      0.155206
      0.175344
      0.197986
      0.0
      0.197986
      0.317136
      0.483328
      0.689705
      0.302586
      0.153650
      0.237950
      0.865758
      0.812120
      0.583075
      0.787242
      0.0
      0.383840
      0.440115
      0.373946
      0.430963
      0.471428
      0.460249
      0.0
      0.460249
      0.444606
      0.497993
      0.406583
      0.406167
      0.463870
      0.403142
      0.234360
      0.388152
      0.397824
      0.364322
    
    
      37
      RRBS_cw154_Tris_protease_CTCTCTAC.GCTGCC.dan.anno
      0.0
      0.549865
      0.375639
      0.572812
      0.150089
      0.162113
      0.164505
      0.0
      0.164505
      0.324149
      0.608583
      0.611432
      0.317604
      0.143925
      0.240400
      0.757844
      0.797200
      0.527989
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66 rows × 39 columns



In [118]:

    
cw154 = cw154.drop(cw154.index[[11, 18, 29, 51]])



In [121]:

    
cw154 = cw154.reset_index()



In [122]:

    
cw154.shape









    Out[122]:





(62, 40)



In [123]:

    
cw154.to_csv("Correct_cw154_regions.csv", index=False)



In [124]:

    
print(normalB.shape)
print(mcell.shape)
print(pcell.shape)
print(cd19cell.shape)
print(trito.shape)
print(cw154.shape)









    



(113, 40)
(75, 40)
(70, 40)
(84, 40)
(42, 40)
(62, 40)



In [125]:

    
113+70+75+84









    Out[125]:





342



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