Python 2.6.5 (r265:79063, Apr 16 2010, 13:09:56) 
[GCC 4.4.3] on linux2
Type "copyright", "credits" or "license()" for more information.

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IDLE 2.6.5      
>>> matrix = [[1,2,3,4],[5,6,7,8],[9,10,11,12]]
>>> matrix
[[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12]]
>>> matrix[0]
[1, 2, 3, 4]
>>> matrix[0][0]
1
>>> matrix[2][1]
10
>>> import filetest
>>> lines = filetest.readtdt("supp2data.tdt")
>>> lines[3]
'YLR292C\tSEC72  SECRETION        ER PROTEIN TRANSLOCATION SUBCOMPLEX SUBUNIT\t-0.23\t0.19\t-0.36\t0.14\t-0.4\t0.16\t-0.09\t-0.12\t-0.14\t-0.14\t-0.38\t-0.22\t0.12\t-0.43\t-0.42\t-0.45\t-0.17\t-0.27\t0.29\t-0.09\t0.4\t-0.1\t0.46\t0.15\t-0.17\t-0.18\t-0.07\t-0.34\t0.3\t-0.12\t-0.06\t-0.17\t0.07\t0.38\t0.34\t\t-0.15\t-0.2\t0.19\t0.37\t0.24\t-0.07\t\t0.24\t0.45\t0.23\t0.5\t-0.07\t\t0.66\t0.94\t0.46\t0.06\t-0.18\t0.39\t-0.18\t0.16\t0.55\t-0.06\t-0.94\t0.21\t-0.71\t-0.86\t-0.45\t0.42\t1.04\t0.65\t0.53\t-0.47\t0.21\t-0.29\t-0.36\t-0.1\t-0.29\t-0.18\t-0.34\t-0.47\t-0.43\t-1.06\n'
>>> lines[3].split("\t")
['YLR292C', 'SEC72  SECRETION        ER PROTEIN TRANSLOCATION SUBCOMPLEX SUBUNIT', '-0.23', '0.19', '-0.36', '0.14', '-0.4', '0.16', '-0.09', '-0.12', '-0.14', '-0.14', '-0.38', '-0.22', '0.12', '-0.43', '-0.42', '-0.45', '-0.17', '-0.27', '0.29', '-0.09', '0.4', '-0.1', '0.46', '0.15', '-0.17', '-0.18', '-0.07', '-0.34', '0.3', '-0.12', '-0.06', '-0.17', '0.07', '0.38', '0.34', '', '-0.15', '-0.2', '0.19', '0.37', '0.24', '-0.07', '', '0.24', '0.45', '0.23', '0.5', '-0.07', '', '0.66', '0.94', '0.46', '0.06', '-0.18', '0.39', '-0.18', '0.16', '0.55', '-0.06', '-0.94', '0.21', '-0.71', '-0.86', '-0.45', '0.42', '1.04', '0.65', '0.53', '-0.47', '0.21', '-0.29', '-0.36', '-0.1', '-0.29', '-0.18', '-0.34', '-0.47', '-0.43', '-1.06\n']
>>> import filetest2
>>> cells = filetest2.readCells("supp2data.txt")

Traceback (most recent call last):
  File "<pyshell#10>", line 1, in <module>
    cells = filetest2.readCells("supp2data.txt")
  File "/home/karmic/Projects/Courses/BmsMinicourse/examples2/filetest2.py", line 2, in readCells
    fp = open(filename)
IOError: [Errno 2] No such file or directory: 'supp2data.txt'
>>> cells = filetest2.readCells("supp2data.tdt")
>>> len(cells)
2468
>>> len(cells[0])
81
>>> cells[0]
['ORF', 'NAME', 'alpha 0', 'alpha 7', 'alpha 14', 'alpha 21', 'alpha 28', 'alpha 35', 'alpha 42', 'alpha 49', 'alpha 56', 'alpha 63', 'alpha 70', 'alpha 77', 'alpha 84', 'alpha 91', 'alpha 98', 'alpha 105', 'alpha 112', 'alpha 119', 'Elu 0', 'Elu 30', 'Elu 60', 'Elu 90', 'Elu 120', 'Elu 150', 'Elu 180', 'Elu 210', 'Elu 240', 'Elu 270', 'Elu 300', 'Elu 330', 'Elu 360', 'Elu 390', 'cdc15 10', 'cdc15 30', 'cdc15 50', 'cdc15 70', 'cdc15 90', 'cdc15 110', 'cdc15 130', 'cdc15 150', 'cdc15 170', 'cdc15 190', 'cdc15 210', 'cdc15 230', 'cdc15 250', 'cdc15 270', 'cdc15 290', 'spo 0', 'spo 2', 'spo 5', 'spo 7', 'spo 9', 'spo 11', 'spo5 2', 'spo5 7', 'spo5 11', 'spo- early', 'spo- mid', 'heat 0', 'heat 10', 'heat 20', 'heat 40', 'heat 80', 'heat 160', 'dtt 15', 'dtt 30', 'dtt 60', 'dtt 120', 'cold 0', 'cold 20', 'cold 40', 'cold 160', 'diau a', 'diau b', 'diau c', 'diau d', 'diau e', 'diau f', 'diau g\n']
>>> cells[5]
['YIL118W', 'RHO3   CYTOSKELETON        GTP-BINDING PROTEIN, RHO FAMILY', '0.04', '0.01', '-0.81', '', '-0.3', '0.49', '0.08', '0.19', '-0.03', '-0.32', '-0.34', '-0.22', '-0.03', '-0.06', '0.06', '0.07', '0.1', '0.03', '-0.18', '-0.2', '-0.12', '0.16', '-0.17', '0.1', '-0.14', '-0.01', '-0.15', '0.04', '0.23', '-0.04', '0.07', '0.06', '0.7', '0.36', '0.37', '0.3', '-0.04', '0.19', '-0.45', '0.21', '-1.12', '-0.04', '0.3', '0.88', '-0.49', '-0.23', '-0.04', '-0.2', '0.45', '0.52', '0.62', '0.48', '0.65', '-0.14', '-0.14', '-0.49', '-0.04', '0.14', '-0.1', '-0.2', '0.01', '-0.4', '-0.23', '-0.04', '0.25', '-0.27', '0.1', '0.1', '-0.2', '0.28', '-0.17', '0.26', '0.07', '-0.17', '', '-0.1', '-0.23', '-0.51', '-1.4\n']
>>> cells[0][5]
'alpha 21'
>>> cell[50][50]

Traceback (most recent call last):
  File "<pyshell#17>", line 1, in <module>
    cell[50][50]
NameError: name 'cell' is not defined
>>> cells[50][50]
'0.7'
>>> float(cells[50][50])
0.69999999999999996
>>> cells[0][50]
'spo 2'
>>> float(cells[0][50])

Traceback (most recent call last):
  File "<pyshell#21>", line 1, in <module>
    float(cells[0][50])
ValueError: invalid literal for float(): spo 2
>>> def coerce(x):
	try:
		return float(x)
	except:
		return None

	
>>> a = coerce("20")
>>> a
20.0
>>> a = coerce("twenty")
>>> a
>>> a == None
True
>>> def coerce(x):
	try:
		a = float(x)
		import math
		return math.log(a)/math.log(2)
	except:
		return None

	
>>> coerce("4")
2.0
>>> coerce(4)
2.0
>>> coerce("twenty")
>>> coerce("-2.0")
>>> import rpy
>>> x = rpy.r.rnorm(200)
>>> x
[0.49034386638608113, 0.44002968846141038, -0.60041281602687357, -0.27219686405667703, -0.31455473628758962, -0.37658325142684529, -1.3105074921959539, -1.7163152936048012, -0.5795842964294815, -1.1076354276959648, 0.18795933011984148, 0.68854487466868108, -0.27514816307013668, 1.3897140056496364, 0.6045683149921236, 0.76515157496587227, 1.4778508830503587, -0.05199030051442164, -0.68798817541282209, 0.46089413523484929, 0.66353704608494746, 1.6178254026421315, 0.91891627470435489, 0.17018308201625723, -1.0761379353404734, -0.76692054909225527, 0.065520441334499746, -0.21308990407614498, -0.82502034636654986, -1.937349180764163, -0.16972077654143822, 0.94278058074466742, 0.38452169872565911, 0.12932002820113825, 0.28090401396878634, 2.0392662978543572, 0.2340767946764809, -0.70316198736359314, -0.19880620634987015, -0.87125626724851324, 0.47542446717316095, 0.96486904721655908, 0.87141942305241349, -0.21605672361370187, 0.71964920826058454, 0.35472766999172406, 0.12469090544642741, -0.36846400499124193, 0.66682948943903575, 0.086376887876039518, -0.077534199460945599, 1.0719119816019975, -0.57363314827105993, 1.470037471677889, 0.23490597133539384, -1.301632271317448, -0.037464323395782449, -1.6176953438271864, 0.3122895136851852, -1.5378732039671756, -0.39891126304779434, -0.076695490312837414, -0.71028226949124973, -0.97318076274851217, 0.48259326687860676, 0.37712807372654816, -0.14336466660973957, 0.42463391786287724, 0.58279642559185996, -0.94540696907783095, 0.34432964471912725, 0.70130143490968866, -0.72023455233450506, -0.28165950546780177, 0.07725664341622851, 1.3527507638132268, -0.74185916507148753, -0.47879875967961166, -0.48577163390341066, 1.2331352017877906, 1.0811325930516422, -0.12430484650081813, 1.0005283801581208, 1.0499715698842671, 0.48970698763526255, 1.4509892455447078, 0.21025240205749107, 0.66832211192187418, 1.3829229576405817, 0.98233717280168364, -0.33674040435929548, -0.84030085416881117, 0.82529851767835261, -1.2880447776742676, -1.457120047255142, 0.97924929911239955, -1.4591738715064848, -1.2466414366567535, -0.32255249201596986, -1.1618756826312799, -0.98025638056582565, -0.57800409986274714, -1.24158580050086, 0.25216522692358012, -0.20077527742840551, -1.6719612293579174, -1.752016878273394, 2.1962809303540007, 2.0274521150116946, -0.63816664679746804, 0.91560165979334218, -0.95580006433628806, -0.99406118561969736, 1.8272526988740079, -1.0026601872148084, 0.87727350097801937, -1.7216099445042077, 0.13499023390339698, 0.28112347496372891, 0.65205944127878646, 0.78486954884255955, 0.34109444132112077, -0.88885815156518111, -1.0820243568280652, -0.06655994756874524, 0.6599063588016697, -0.70118692914606628, -0.051812332434018775, 0.67318455929654653, 0.11075204793310305, -1.9453898576830686, 0.72675965790793806, -1.623964819465848, 1.5724970363311059, 0.93577242166042851, 0.47881901610857541, 0.43498881795465244, -1.414862507848663, 0.51597239681370932, 0.45805086855181815, 0.66891813725758131, 0.34220686997887739, 1.2106618886564966, 1.1138498653570807, -1.0315885155354529, 1.2504160479028823, 0.88230531885724439, 0.44212767566407207, 0.37847901637503428, -1.6957852821986867, 1.1138224135831865, 0.578446646360947, 1.2983253754482049, 0.14224241369874835, -0.66799317675439041, -0.19328135652535414, 0.34027477370839376, 0.17658245286779464, 1.1539552313050601, -1.1953547254015666, -0.037018407343747652, -0.62695782704982805, 0.96703847356703887, -1.1976017322915518, -0.97788969401260761, 0.72634978616111212, -0.34304175818837879, 1.9543611961548022, -0.93364478360501368, 0.84817692106804532, -0.20350071202528489, 0.33950954623254281, -0.18652751777872106, -0.44314639160931879, 0.46974212034923979, 0.67928769021888236, -0.50360374392181639, 1.0257702593449807, -0.020763275517118089, -0.45047783096668476, 0.39570336307647402, -0.10093255024489242, 0.0001095118853529658, 0.95857090003167256, 1.3335895030950695, -1.9669403455275072, 1.2124500349788794, 0.30787129915679612, 0.33779973668130958, -1.5081651827024072, 1.442702125095698, -0.67171154083533846, -0.67046776463766278, -0.37134704924507661, 2.3734241623650174, 0.26743012804699801, 0.0032707385859051517, -1.3853753216590936, 1.5728773731301415, -0.76439714960063931]
>>> y = rpy.r.rnorm(200)
>>> rpy.r.pdf("test.pdf")
>>> rpy.r.plot(x,y,xlab = "x", ylab = "y")
>>> rpy.r.dev_off()
{'null device': 1}
>>>