[SciPy-User] Error: numpy/lib/recfunctions.py line 755, in find_duplicates sorteddata = sortedbase.filled()

[Vincent Davis]

Not sure what is going on here but am am getting an error that I am not sure
how to fix. Any Help world me appreciated.

>>> masteromni
array([ ('AMA1_CDS_st', 'AMA1_CDS_st:389:30', 389, 30, 13, 0, 1,
'AGCCTCCCATGATTGAACAGATCAT', 'Sense', 'PM', 'Tiling', 0.3911,
61.700000000000003, 44.0, -38.661999999999999, -193.69999999999999, -520.0,
'AMA_CDS', 1, 'VIIb', 4880893, 4880869, 4880881,
'TGME49_chrVIIb:4880893..4880869', ' empt'),
       ('AMA1_CDS_at', 'AMA1_CDS_at:45:44', 45, 44, 15, 0, 1,
'GATCTGTTCAATCATGGGAGGCTTG', 'Antisense', 'PM', 'Tiling', 0.437,
61.899999999999999, 48.0, -38.825000000000003, -194.40000000000001,
-521.79999999999995, 'AMA_CDS', 2, 'VIIb', 4880871, 4880895, 4880883,
'TGME49_chrVIIb:4880871..4880895', ' empt'),
       ('AMA1_CDS_st', 'AMA1_CDS_st:116:84', 116, 84, 17, 1, 2,
'CGCAAGCCTCCCATGATTGAACAGA', 'Sense', 'PM', 'Tiling', 0.57669999999999999,
65.200000000000003, 52.0, -41.142000000000003, -199.40000000000001,
-530.79999999999995, 'AMA_CDS', 3, 'VIIb', 4880897, 4880873, 4880885,
'TGME49_chrVIIb:4880897..4880873', ' empt'),
       ...,
       ('25.m02918_AS_at', '25.m02918_AS_at:24:29', 24, 29, 43214, 17, 18,
'ATGGATGTACATTCGCTGCTGACTA', 'Antisense', 'PM', 'Antisense detection', 0.0,
61.700000000000003, 44.0, -39.125, -197.80000000000001, -532.20000000000005,
'-1', -1, 'Ib', 87103, 87079, 87091, 'TGME49_chrIb:87103..87079', ' empt'),
       ('25.m02918_AS_at', '25.m02918_AS_at:208:333', 208, 333, 43310, 18,
19, 'AGAACTTCCGTGTGCAACTGCTTTA', 'Antisense', 'PM', 'Antisense detection',
0.67410000000000003, 62.899999999999999, 44.0, -39.993000000000002,
-200.09999999999999, -537.0, '-1', -1, 'Ib', 87007, 86983, 86995,
'TGME49_chrIb:87007..86983', ' empt'),
       ('25.m02918_AS_at', '25.m02918_AS_at:435:348', 435, 348, 43550, 19,
20, 'AATAGGCATTTCGTGGTTCGCGCAA', 'Antisense', 'PM', 'Antisense detection',
0.62050000000000005, 65.700000000000003, 48.0, -42.009999999999998,
-204.80000000000001, -546.0, '-1', -1, 'Ib', 86767, 86743, 86755,
'TGME49_chrIb:86767..86743', ' empt')],
      dtype=[('probe_set_name', '|S40'), ('ProbeUniqueName', '|S40'), ('x',
'<i8'), ('y', '<i8'), ('Interrogation_position', '<i8'),
('Probeset_position0', '<i8'), ('Probeset_position1', '<i8'), ('Sequence2',
'|S25'), ('Strandedness', '|S40'), ('PM', '|S40'), ('Purpose', '|S40'),
('AffyProbeScore', '<f8'), ('Tm_emboss', '<f8'), ('gc_emboss', '<f8'),
('DeltaG_emboss', '<f8'), ('DeltaH_emboss', '<f8'), ('DeltaS_emboss',
'<f8'), ('TilingSet', '|S40'), ('AbsTileNum', '<i8'), ('Chr', '|S40'),
('ChrProbeStart2', '<i8'), ('ChrProbeStop2', '<i8'), ('ChrMidpoint', '<i8'),
('GenBrowserCoords', '|S40'), ('emptyColumn', '|S5')])


>>> find_duplicates(omni_snps[:5], 'ProbeUniqueName')
Traceback (most recent call last):
  File
"/Applications/WingIDE.app/Contents/MacOS/src/debug/tserver/_sandbox.py",
line 1, in <module>
    # Used internally for debug sandbox under external interpreter
  File
"/Library/Frameworks/EPD64.framework/Versions/6.1/lib/python2.6/site-packages/numpy/lib/recfunctions.py",
line 755, in find_duplicates
    sorteddata = sortedbase.filled()
AttributeError: 'numpy.ndarray' object has no attribute 'filled'


  *Vincent Davis
720-301-3003 *
vincent at vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.scipy.org/pipermail/scipy-user/attachments/20100313/48cc2cf1/attachment.html>