Create a file formatted for visualization in the R package methylKit

M1

In [3]: 
!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M1_tab.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_M1.txt
In [4]: 
#Second line of code for creating a formatted file for methylKit
!tr ' ' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_M1.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M1final.txt
In [5]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M1final.txt

C12768	103	104	+	6	0.166667	0.833333
C12806	76	77	+	5	0.2	0.8
C12806	78	79	+	5	0.2	0.8
C12806	142	143	+	8	0.375	0.625
C12924	30	31	+	5	0	1
C12924	38	39	+	5	0	1
C12924	52	53	+	6	0	1
C12924	60	61	+	6	0	1
C12924	127	128	+	6	0	1
C12924	136	137	+	6	0	1

M3

In [6]: 
!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_M3_tab.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_M3.txt
In [7]: 
#Second line of code for creating a formatted file for methylKit
!tr ' ' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_M3.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M3final.txt
In [8]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_M3final.txt

C13128	87	88	+	5	0	1
C13208	83	84	+	7	0.428571	0.571429
C13220	164	165	+	6	0	1
C13442	65	66	+	5	0	1
C13442	79	80	+	5	0	1
C13612	89	90	+	5	0	1
C13992	54	55	+	5	0	1
C14180	158	159	+	5	0	1
C14220	96	97	+	12	0	1
C14220	143	144	+	7	0	1

T1D3

In [9]: 
!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T1D3_tab.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T1D3.txt
In [10]: 
#Second line of code for creating a formatted file for methylKit
!tr ' ' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T1D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T1D3final.txt
In [11]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T1D3final.txt

C12960	123	124	+	8	0	1
C13766	145	146	+	6	0	1
C14468	214	215	+	6	0.166667	0.833333
C14468	216	217	+	6	0.166667	0.833333
C14796	69	70	+	5	1	0
C14952	148	149	+	5	0	1
C14966	42	43	+	5	0.2	0.8
C14966	54	55	+	5	0.2	0.8
C15814	226	227	+	5	0	1
C15834	91	92	+	5	0	1

T1D5

In [12]: 
!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T1D5_tab.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T1D5.txt
In [13]: 
#Second line of code for creating a formatted file for methylKit
!tr ' ' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T1D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T1D5final.txt
In [14]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T1D5final.txt

C12960	67	68	+	5	0	1
C12960	123	124	+	8	0	1
C13766	126	127	+	9	0	1
C13766	145	146	+	10	0	1
C14220	96	97	+	5	0	1
C14220	143	144	+	5	0	1
C14796	69	70	+	8	0.75	0.25
C14886	55	56	+	5	0	1
C14944	199	200	+	7	0	1
C14944	214	215	+	7	0	1

T3D3

In [15]: 
!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T3D3_tab.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T3D3.txt
In [16]: 
#Second line of code for creating a formatted file for methylKit
!tr ' ' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T3D3.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T3D3final.txt
In [17]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T3D3final.txt

C12960	123	124	+	7	0	1
C13546	41	42	+	7	0	1
C13546	84	85	+	7	0	1
C13992	120	121	+	6	0	1
C14180	114	115	+	5	0	1
C14180	125	126	+	5	0	1
C14180	130	131	+	5	0	1
C14180	158	159	+	5	0	1
C14220	96	97	+	7	0	1
C14220	143	144	+	12	0	1

T3D5

In [18]: 
!awk '{print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methratio_out_CG5x_T3D5_tab.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T3D5.txt
In [19]: 
#Second line of code for creating a formatted file for methylKit
!tr ' ' "\t" </Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylkit_out_T3D5.txt> /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T3D5final.txt
In [20]: 
!head /Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/methylKit/methylkit_out_T3D5final.txt

C13220	164	165	+	5	0	1
C13490	83	84	+	5	0	1
C13546	84	85	+	8	0	1
C14220	96	97	+	5	0	1
C14220	143	144	+	5	0	1
C14450	60	61	+	6	0	1
C14450	94	95	+	5	0	1
C14450	106	107	+	6	0	1
C14450	118	119	+	5	0	1
C14450	187	188	+	6	0.166667	0.833333
In []: