First, please specify a local directory where we can save the data to.
In [1]:
%cd /Users/elizabethasmith/Desktop/sql
/Users/elizabethasmith/Desktop/sql
The script 'getSQLdata.py' will pull data from the MySQL database using the following syntax:
If you successfully pull data, you will get a notification summary.
In [3]:
%run getSQLdata.py SXT_datamatrix Mouse_Cells_ALL;
Retrieving data from the Mouse_Cells_ALL; table from the SXT_datamatrix My SQL database...
Success! You just pulled out 26 rows, each of which contained 39 columns, of data.
You also pulled out 39 field names.
These data have been saved in a pandas Dataframe called SXT_datamatrix_Mouse_Cells_ALL;_2015-01-05_12-48-32.npy locally at /Users/elizabethasmith/Desktop/sql.
The Dataframe is also present as a global variable called "df".
Check that this is the data you are intending to pull by displaying the data as a table.
In [5]:
df
Out[5]:
idMouse_Cells_
CellType
Volume_of_Nucleus_(um^3)
Volume_of_ECR_(um^3)
Volume_of_HCR_(µm^3)
Volume_of_Nucleoli_(µm^3)
%_Nuclear_Volume_ECR
%_Nuclear_Volume_HCR
%_Nuclear_Volume_Nucleoli
Surface_Area_Nuclear_Envelope_(µm^2)
...
Polarity_of_HCR_(µm)
Mean_Radius_of_HCR_(µm)
Max_Radius_of_HCR_(µm )
Complexity_HCR_Skeleton
Fractal_Dimension_of_HCR
Error_Fractal_Dimension_of_HCR
Fractal_Dimension_of_Nucleus
Error_Fractal_Dimension_of_Nucleus
%_HCR_Central
%_HCR_Peripheral
0
2
B-Lymphocyte
66.3449
27.2668
39.0780
0.784957
41.0986
58.9014
1.183150
83.6144
...
0.145258
0.484488
0.96
9013
2.71135
0.295190
2.57205
0.219156
68.63620
0.738725
1
4
cancer
383.7490
305.1100
78.6396
42.853100
79.5076
20.4924
11.167000
346.9600
...
1.281950
0.168585
0.36
14080
2.78040
0.188539
2.28234
0.134772
5.53197
0.501269
2
2
B-Lymphocyte
66.3449
27.2668
39.0780
0.784957
41.0986
58.9014
1.183150
83.6144
...
0.145258
0.484488
0.96
9013
2.71135
0.295190
2.57205
0.219156
68.63620
0.738725
3
2
B-Lymphocyte
170.1640
76.9439
93.2197
0.427622
45.2176
54.7824
0.251301
164.0300
...
0.125474
0.302631
0.60
56449
2.79671
0.197425
2.63880
0.122275
57.08800
0.759885
4
2
B-Lymphocyte
74.4857
33.2654
41.2203
1.000310
44.6601
55.3399
1.342950
92.5136
...
0.235226
0.383058
0.84
7294
2.73169
0.268770
2.57514
0.197709
38.48460
0.802155
5
2
B-Lymphocyte
83.9752
37.6468
46.3284
1.685450
44.8309
55.1691
2.007090
102.2480
...
0.140074
0.310424
0.66
9351
2.74968
0.247996
2.59137
0.170459
26.80100
0.887208
6
2
B-Lymphocyte
87.8655
44.2304
43.6351
0.363561
50.3388
49.6612
0.413770
98.1634
...
0.050914
0.301871
0.66
10063
2.77685
0.213452
2.59283
0.132897
28.77840
0.832397
7
2
B-Lymphocyte
99.4286
46.2350
53.1936
0.895058
46.5007
53.4993
0.900201
106.7120
...
0.076018
0.297503
0.60
11537
2.80457
0.158139
2.63822
0.090558
30.13090
0.888489
8
2
B-Lymphocyte
83.6783
39.8066
43.8717
1.452340
47.5710
52.4290
1.735630
95.3044
...
0.053029
0.292899
0.54
7831
2.75285
0.248884
2.58352
0.172264
21.42560
0.856311
9
2
B-Lymphocyte
82.1372
34.3073
47.8298
0.793805
41.7683
58.2317
0.966438
92.9574
...
0.200282
0.406702
0.78
8003
2.76087
0.236026
2.61979
0.171701
36.97100
0.857541
10
2
B-Lymphocyte
83.1241
39.2170
43.9071
0.940179
47.1789
52.8211
1.131050
93.7042
...
0.214126
0.315426
0.66
8809
2.75842
0.235090
2.59142
0.157562
25.79490
0.804309
11
2
B-Lymphocyte
81.4445
37.7457
43.6988
1.175320
46.3452
53.6548
1.443100
93.5608
...
0.184324
0.322724
0.66
8192
2.76282
0.232276
2.59804
0.158318
24.40790
0.861210
12
2
B-Lymphocyte
182.9390
87.0021
95.9371
6.005490
47.5579
52.4421
3.282780
176.4970
...
0.057729
0.224031
0.48
39205
2.80072
0.192027
2.61727
0.091056
52.18690
0.781224
13
2
B-Lymphocyte
81.4760
39.9664
41.5097
0.335872
49.0529
50.9471
0.412234
94.5835
...
0.059173
0.326499
0.72
9617
2.75482
0.227982
2.58084
0.150269
32.89930
0.737986
14
2
B-Lymphocyte
169.9990
75.3618
94.6377
3.038480
44.3306
55.6694
1.787350
186.1500
...
0.157061
0.220230
0.42
36269
2.77015
0.225247
2.60809
0.141621
37.32130
0.889454
15
2
B-Lymphocyte
89.6586
38.8897
50.7689
0.409534
43.3753
56.6247
0.456771
100.5050
...
0.115619
0.381315
0.90
11981
2.74048
0.266501
2.58886
0.189717
70.47850
0.894204
16
4
cancer
383.7490
305.1100
78.6396
42.853100
79.5076
20.4924
11.167000
346.9600
...
1.281950
0.168585
0.36
14080
2.78040
0.188539
2.28234
0.134772
5.53197
0.501269
17
4
cancer
487.6410
372.6610
114.9800
49.294100
76.4212
23.5788
10.108700
368.5860
...
0.935590
0.131836
0.30
14356
2.78148
0.212586
2.27016
0.138213
7.02035
0.649011
18
4
cancer
564.9000
424.9080
139.9920
65.026700
75.2183
24.7817
11.511200
433.0470
...
0.577048
0.138134
0.42
21151
2.79645
0.187166
2.32407
0.135948
14.32380
0.670322
19
4
cancer
426.3120
335.1450
91.1672
48.250300
78.6149
21.3851
11.318100
401.5500
...
0.958430
0.128145
0.36
14739
2.74686
0.238286
2.24878
0.058154
11.69410
0.541978
20
4
cancer
538.9410
420.8060
118.1350
65.086100
78.0802
21.9198
12.076700
441.6120
...
0.888652
0.142342
0.36
17525
2.77401
0.212259
2.28357
0.100752
8.92096
0.602442
21
4
cancer
395.7650
292.8780
102.8860
49.395000
74.0032
25.9969
12.480900
323.6970
...
0.314256
0.137923
0.36
17498
2.79919
0.168569
2.33824
0.129106
16.62110
0.647063
22
4
cancer
240.1110
175.3480
64.7631
20.242400
73.0279
26.9721
8.430430
264.0230
...
0.550396
0.147141
0.42
21622
2.77532
0.191421
2.31954
0.131400
18.06150
0.511723
23
4
cancer
429.3920
351.0900
78.3012
48.550400
81.7646
18.2354
11.306800
388.7100
...
0.554938
0.111849
0.24
12949
2.77590
0.193416
2.19149
0.151996
6.21968
0.426768
24
4
cancer
502.3070
417.0520
85.2556
50.418400
83.0272
16.9728
10.037400
384.8480
...
1.737040
0.148494
0.30
16608
2.78499
0.203592
2.24298
0.080180
8.41715
0.531860
25
4
cancer
445.8060
375.8240
69.9819
62.807400
84.3022
15.6978
14.088500
454.5160
...
0.692527
0.127219
0.36
11365
2.73899
0.237241
2.13696
0.149920
10.35420
0.339770
26 rows × 39 columns
In [ ]:
Content source: elizabethizzysmith/python_mySQL
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