MustoeLab · minhkhoadao97 · Jan 13, 2026 · Feb 9, 2026
diff --git a/.DS_Store b/.DS_Store
diff --git a/ArcPlot.py b/ArcPlot.py
@@ -1481,7 +1481,7 @@ def merge_peak(group):
 
         df = df.sort_values(by = ['info', 'tstart'])
         df = df.groupby('info').apply(lambda g: merge_peak(g))
-        df = df.groupby(['info', 'diff']).agg({'tstart': 'min', 'tend': 'max'}).reset_index()
+        df = df.groupby([pd.Grouper(key='info'), 'diff']).agg({'tstart': 'min', 'tend': 'max'}).reset_index()
         df = df.sort_values(by = 'info')
         df['label'], df['group'] = zip(*df['info'].apply(lambda g: split_info(g)))
 

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diff --git a/ENCODE_eCLIP_data/ENCFF985ECA.bed.gz b/ENCODE_eCLIP_data/ENCFF985ECA.bed.gz
diff --git a/ENCODE_eCLIP_data/ENCFF986XOC.bed.gz b/ENCODE_eCLIP_data/ENCFF986XOC.bed.gz
diff --git a/ENCODE_eCLIP_data/ENCFF992LCW.bed.gz b/ENCODE_eCLIP_data/ENCFF992LCW.bed.gz
diff --git a/ENCODE_eCLIP_data/ENCFF993VRZ.bed.gz b/ENCODE_eCLIP_data/ENCFF993VRZ.bed.gz
diff --git a/ENCODE_eCLIP_data/ENCFF999ZAW.bed.gz b/ENCODE_eCLIP_data/ENCFF999ZAW.bed.gz
diff --git a/ExampleData/.DS_Store b/ExampleData/.DS_Store
diff --git a/ExampleData/7SKexample/.Rhistory b/ExampleData/7SKexample/.Rhistory
diff --git a/ExampleData/7SKexample/7SK-incell-0-pairmap.txt b/ExampleData/7SKexample/7SK-incell-0-pairmap.txt
@@ -0,0 +1,46 @@
+332	Window=3	Metric=PAIRMAPPER	
+i	j	Sig.	Class	Zij	Zi	Zj	Mod_Depth	Mod_Comuts	Unt_Depth	Unt_Comuts
+94	168	240.20	1	7.84	8.09	7.59	437910	1439	3372303	195
+114	149	46.92	1	5.16	5.02	5.30	459229	163	3390869	64
+115	148	27.60	1	3.08	2.81	3.35	457204	136	3380099	76
+116	147	25.63	1	3.17	1.83	4.50	458532	177	3393820	151
+122	137	106.61	1	6.61	3.71	9.50	446552	89	3396881	56
+123	136	44.30	1	5.02	6.93	3.11	452981	312	3395564	50
+201	271	53.03	1	4.31	4.05	4.56	449541	565	3376393	333
+206	266	31.37	1	3.06	4.35	1.78	450649	327	3370770	143
+212	260	63.23	1	5.32	7.14	3.49	453225	295	3377420	307
+213	259	83.43	1	6.69	9.86	3.53	449141	225	3378323	81
+32	41	84.82	2	7.82	4.27	11.38	434861	309	3264424	49
+59	71	24.06	2	2.83	4.11	1.54	441387	946	3272323	128
+60	70	167.27	2	9.16	8.91	9.40	440914	1273	3271747	241
+67	80	70.95	2	4.73	5.23	4.24	387077	3797	3265721	121
+67	285	56.25	2	3.20	4.15	2.25	419938	4468	3275920	25
+78	104	43.87	2	2.96	2.41	3.51	379919	4012	3277608	242
+79	103	60.32	2	3.90	3.44	4.37	382533	5214	3283356	122
+89	187	33.91	2	2.75	2.20	3.30	455119	2272	3397833	480
+92	167	168.27	2	4.34	4.16	4.51	439501	1509	3395327	109
+93	169	123.19	2	3.67	2.86	4.48	428367	1362	3396600	175
+95	167	149.08	2	6.25	8.50	4.00	438321	1430	3396565	229
+109	154	573.36	2	11.92	10.43	13.42	435314	3270	3385166	91
+170	223	113.84	2	2.70	4.29	1.10	428667	1866	3391299	339
+171	183	222.24	2	6.22	7.73	4.71	436764	1772	3372402	35
+172	182	32.34	2	3.44	1.04	5.85	438222	510	3391204	51
+202	260	55.49	2	3.88	4.69	3.07	451585	304	3354992	178
+211	261	102.29	2	6.47	6.35	6.59	453611	279	3386086	214
+221	251	192.97	2	4.67	4.93	4.40	439369	2685	3387419	166
+222	253	95.62	2	2.52	3.00	2.05	422407	1015	3371146	126
+226	246	51.04	2	5.08	3.29	6.87	430995	883	3386704	54
+228	248	56.80	2	4.18	0.90	7.46	432936	819	3378308	20
+229	247	46.11	2	2.87	0.53	5.21	434073	1017	3358693	11
+247	260	27.03	2	2.27	3.06	1.49	452872	217	3380118	108
+248	259	24.43	2	2.12	3.21	1.03	445852	120	3371503	32
+60	104	29.38	0	1.96	1.57	2.35	410639	1895	3279289	315
+60	176	25.07	0	2.04	1.34	2.73	427107	2479	3264914	356
+61	200	23.90	0	1.31	1.49	1.13	433068	709	3267858	128
+64	176	28.62	0	3.30	3.47	3.12	417262	4344	3207950	184
+64	183	26.69	0	1.90	3.24	0.57	416303	1889	3214114	53
+66	286	80.71	0	4.21	4.79	3.63	426152	9572	3272850	49
+80	102	26.66	0	1.77	1.59	1.95	379188	3738	3279879	187
+83	193	26.44	0	2.87	4.43	1.30	409310	2044	3146869	35
+98	165	69.51	0	4.01	2.80	5.22	433883	2983	3385485	65
+223	252	43.40	0	0.67	0.41	0.93	433943	1508	3385274	314
diff --git a/ExampleData/7SKexample/7SK-incell-0-rings.txt b/ExampleData/7SKexample/7SK-incell-0-rings.txt
diff --git a/ExampleData/7SKexample/7SK-incell-0.ct b/ExampleData/7SKexample/7SK-incell-0.ct
@@ -0,0 +1,333 @@
+  332  ENERGY = -153.8  sequence
+    1 G       0    2  295    1
+    2 G       1    3  294    2
+    3 A       2    4  293    3
+    4 U       3    5  292    4
+    5 G       4    6  291    5
+    6 U       5    7  290    6
+    7 G       6    8  289    7
+    8 A       7    9    0    8
+    9 G       8   10    0    9
+   10 G       9   11   48   10
+   11 G      10   12   47   11
+   12 C      11   13   46   12
+   13 G      12   14   45   13
+   14 A      13   15   44   14
+   15 U      14   16   43   15
+   16 C      15   17   42   16
+   17 U      16   18   39   17
+   18 G      17   19   38   18
+   19 G      18   20   37   19
+   20 C      19   21    0   20
+   21 U      20   22    0   21
+   22 G      21   23    0   22
+   23 C      22   24    0   23
+   24 G      23   25   33   24
+   25 A      24   26   32   25
+   26 C      25   27   31   26
+   27 A      26   28    0   27
+   28 U      27   29    0   28
+   29 C      28   30    0   29
+   30 U      29   31    0   30
+   31 G      30   32   26   31
+   32 U      31   33   25   32
+   33 C      32   34   24   33
+   34 A      33   35    0   34
+   35 C      34   36    0   35
+   36 C      35   37    0   36
+   37 C      36   38   19   37
+   38 C      37   39   18   38
+   39 A      38   40   17   39
+   40 U      39   41    0   40
+   41 U      40   42    0   41
+   42 G      41   43   16   42
+   43 A      42   44   15   43
+   44 U      43   45   14   44
+   45 C      44   46   13   45
+   46 G      45   47   12   46
+   47 C      46   48   11   47
+   48 C      47   49   10   48
+   49 A      48   50    0   49
+   50 G      49   51    0   50
+   51 G      50   52    0   51
+   52 G      51   53    0   52
+   53 U      52   54    0   53
+   54 U      53   55    0   54
+   55 G      54   56    0   55
+   56 A      55   57    0   56
+   57 U      56   58    0   57
+   58 U      57   59    0   58
+   59 C      58   60   73   59
+   60 G      59   61   72   60
+   61 G      60   62   71   61
+   62 C      61   63   70   62
+   63 U      62   64   69   63
+   64 G      63   65    0   64
+   65 A      64   66    0   65
+   66 U      65   67    0   66
+   67 C      66   68    0   67
+   68 U      67   69    0   68
+   69 G      68   70   63   69
+   70 G      69   71   62   70
+   71 C      70   72   61   71
+   72 U      71   73   60   72
+   73 G      72   74   59   73
+   74 G      73   75    0   74
+   75 C      74   76    0   75
+   76 U      75   77    0   76
+   77 A      76   78    0   77
+   78 G      77   79   93   78
+   79 G      78   80   92   79
+   80 C      79   81    0   80
+   81 G      80   82   90   81
+   82 G      81   83   89   82
+   83 G      82   84   88   83
+   84 U      83   85    0   84
+   85 G      84   86    0   85
+   86 U      85   87    0   86
+   87 C      86   88    0   87
+   88 C      87   89   83   88
+   89 C      88   90   82   89
+   90 C      89   91   81   90
+   91 U      90   92    0   91
+   92 U      91   93   79   92
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