outputting python/numpy arrays as columns

Question

I'm very new to python, but have been using it to calculate and filter through data. I'm trying to output my array so I can pass it to other programs, but the output is one solid piece of text, with brackets and commas separating it.

I understand there are ways of manipulating this, but I want to understand why my code has output it in this format, and how to make it output it in nice columns instead.

The array was generated with:

! /usr/bin/env python

import numpy as np
import networkx
import gridData
from scipy.spatial.distance import euclidean

INPUT1=open("test_area.xvg",'r')
INPUT2=open("test_atom.xvg",'r')
OUTPUT1= open("negdist.txt",'w')

area = []
pointneg = []
posneg = []
negdistance =[ ]
negresarea = []

 while True:
      line = INPUT1.readline()
      if not line:
           break
      col = line.split()
      if col:
            area.append(((col[0]),float(col[1])))


 pointneg.append((-65.097000,5.079000,-9.843000))



while True:
    line = INPUT2.readline()
    if not line:
         break
    col = line.split()
    if col:
         pointneg.append((float(col[5]),float(col[6]),float(col[7])))
         posneg.append((col[4]))


 for col in posneg:
      negresarea.append(area[int(col)-1][1])


 a=len(pointneg)

 for x in xrange(a-1):

        negdistance.append((-1,(negresarea[x]),euclidean((pointneg[0]),(pointneg[x]))))

  print >> OUTPUT1, negdistance

example output:

[(-1, 1.22333, 0.0), (-1, 1.24223, 153.4651968428021), (-1, 1.48462, 148.59335545709976), (-1, 1.39778, 86.143305392816202), (-1, 0.932278, 47.914688322058403), (-1, 1.04997, 28.622555546282022),

desired output:

[-1, 1.22333, 0.0

-1, 1.24223, 153.4651968428021

-1, 1.48462, 148.59335545709976

-1, 1.39778, 86.143305392816202

-1, 0.932278, 47.914688322058403 

-1, 1.04997, 28.622555546282022...

Example inputs:

example input1

     1     2.12371          0
     2     1.05275          0
     3    0.865794          0
     4    0.933986          0
     5     1.09092          0
     6     1.22333          0
     7     1.54639          0
     8     1.24223          0
     9     1.10928          0
    10     1.16232          0
    11     0.60942          0
    12     1.40117          0
    13     1.58521          0
    14     1.00011          0
    15     1.18881          0
    16     1.68442          0
    17    0.866275          0
    18     1.79196          0
    19      1.4375          0
    20       1.198          0
    21     1.01645          0
    22     1.82221          0
    23     1.99409          0
    24      1.0728          0
    25    0.679654          0
    26     1.15578          0
    27     1.28326          0
    28     1.00451          0
    29     1.48462          0
    30     1.33399          0
    31     1.13697          0
    32     1.27483          0
    33     1.18738          0
    34     1.08141          0
    35     1.15163          0
    36     0.93699          0
    37    0.940171          0
    38     1.92887          0
    39     1.35721          0
    40     1.85447          0
    41     1.39778          0
    42     1.97309          0

Example Input2

ATOM     35  CA  GLU     6      56.838   -5.202 -102.459  1.00273.53           C
ATOM     55  CA  GLU     8      54.729   -6.650  -96.930  1.00262.73           C
ATOM    225  CA  GLU    29       5.407   -2.199  -58.801  1.00238.62           C
ATOM    321  CA  GLU    41      -24.633   -0.327  -34.928  1.00321.69           C

memebrain · Accepted Answer · 2016-01-17 12:52:02Z

1

The problem is the multiple parenthesis when you append. You are appending tuples.

what you want is to be adding lists - i.e. the ones with square brackets.

import numpy as np
area = []
with open('example2.txt') as filehandle:
    for line in filehandle:
        if line.strip() == '':continue
        line = line.strip().split(',')
        area.append([int(line[0]),float(line[1]),float(line[2])])
    area = np.array(area)
print(area)

'example2.txt' is the data you provided made into a csv

edited Jan 17, 2016 at 12:52

answered Jan 17, 2016 at 11:31

memebrain

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6 Comments

erin_wolf Over a year ago

edited the question to include an example input (which is a truncated version of the full set).

erin_wolf Over a year ago

edited again, so you should have all the information to run it

memebrain Over a year ago

can you tell me where my answer isn't answering your question?

erin_wolf Over a year ago

Sorry, I didn't see that. I was testing a few things while inputing the code and I guess the page didn't show me your edit... Trying it now in the exact code I've supplied above, and for the end argument I still get: [[-1, [1.22333], 0.0], [-1, [1.24223], 153.4651968428021], [-1, [1.48462], 148.59335545709976], [-1, [1.39778], 86.143305392816202]]

memebrain Over a year ago

OK, I'll take another tack. I fail to see how using the print statement can change anything about the operation of your code. You aren't printing to a file. If you put parenthesis around things, you are creating a tuple, an immutable data type. Are you intentionally doing that?

|

erin_wolf · Accepted Answer · 2016-01-17 20:25:22Z

0

I didn't really get an answer that enabled me to understand the problem, the one suggested above just prevented to whole code working properly. I did find a work around by including the print command in the loop defining my final output.

 for x in xrange(a-1):

    negdistance.append((-1,(negresarea[x]),euclidean((pointneg[0]),(pointneg[x]))))
    print negdistance
    negdistance =[]

answered Jan 17, 2016 at 20:25

erin_wolf

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