numpy beginner: writing an array using numpy.savetxt

Question

I have a numpy histogram that I would like to output as a tab-delimited text file. My code is below:

targethist = np.histogram(targetlist, bins=ilist)
print targethist
np.savetxt('ChrI_dens.txt',targethist,delimiter='\t')

targetlist and ilist are long lists of integers. I get the following output:

(array([0, 0, 0, ..., 0, 0, 0]), array([ 1, 10000, 20000, ..., 15060000, 15070000, 15072422])) Traceback (most recent call last): File "target_dens_np.py", line 62, in np.savetxt('ChrI_dens.txt',targethist,delimiter='\t') File "/Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages/numpy/lib/npyio.py", line 979, in savetxt fh.write(asbytes(format % tuple(row) + newline)) TypeError: float argument required, not numpy.ndarray

It seems that the histogram array has been created, but I have done something wrong in the np.savetxt() line. I have read the documentation, but don't understand why any of the arguments in this function would be expecting a float. Where have I gone wrong?

Answer 1

I think that the problem is that the second argument to savetxt must be "array-like". Your input is not "array-like". e.g.

print (len(targethist[0]))
print (len(targethist[1]))

Notice the lengths aren't the same? If the lengths were the same, numpy could convert it to a single 2-D array and everything would be fine, but it can't do the conversion so it fails.

This works

np.savetxt('stuff.dat',(targethist[0],targethist[1][1:]),delimiter='\t')

But I've truncated your data ;). You'll need to decide what you want to do to work around this one.

I must admit, the error message here is quite cryptic.