CODEWITHSUNDEEP
pythoncsv
Chubaka
Chubaka

Reputation: 3155

python csv delimiter doesn't work properly

I try to write a python code to extract DVDL values from the input. Here is the truncated input.

      A V E R A G E S   O V E R   50000 S T E P S


 NSTEP =    50000   TIME(PS) =     300.000  TEMP(K) =   300.05  PRESS =   -70.0
 Etot   =    -89575.9555  EKtot   =     23331.1725  EPtot      =   -112907.1281
 BOND   =       759.8213  ANGLE   =      2120.6039  DIHED      =      4231.4019
 1-4 NB =       940.8403  1-4 EEL =     12588.1950  VDWAALS    =     13690.9435
 EELEC  =   -147238.9339  EHBOND  =         0.0000  RESTRAINT  =         0.0000
 DV/DL  =        13.0462 
 EKCMT  =     10212.3016  VIRIAL  =     10891.5181  VOLUME     =    416404.8626
                                                Density    =         0.9411
 Ewald error estimate:   0.6036E-04



      R M S  F L U C T U A T I O N S


 NSTEP =    50000   TIME(PS) =     300.000  TEMP(K) =     1.49  PRESS =   129.9
Etot   =       727.7890  EKtot   =       115.7534  EPtot      =       718.8344
BOND   =        23.1328  ANGLE   =        36.1180  DIHED      =        19.9971
1-4 NB =        12.7636  1-4 EEL =        37.3848  VDWAALS    =       145.7213
EELEC  =       739.4128  EHBOND  =         0.0000  RESTRAINT  =         0.0000
DV/DL  =         3.7510
EKCMT  =        76.6138  VIRIAL  =      1195.5824  VOLUME     =     43181.7604
                                                Density    =         0.0891
 Ewald error estimate:   0.4462E-04

Here is the script. Basically we have a lot of DVDL in the input (not in the above truncated input) and we only want the last two. So we read all of them into a list and only get the last two. Finally, we write the last two DVDL in the list into a csv file. The desire output is

13.0462, 3.7510

However, the following script (python 2.7) will bring the output like this. Could any guru enlighten? Thanks.

13.0462""3.7510""

Here is the script:

import os
import csv

DVDL=[]
filename="input.out"
file=open(filename,'r')

with open("out.csv",'wb') as outfile: # define output name
    line=file.readlines()
    for a in line:
        if ' DV/DL  =' in a:
            DVDL.append(line[line.index(a)].split('        ')[1])  # Extract DVDL number

    print DVDL[-2:]        # We only need the last two DVDL
    yeeha="".join(str(a) for a in DVDL[-2:])
    print yeeha
    writer = csv.writer(outfile, delimiter=',',lineterminator='\n')#Output the list into a csv file called "outfile"
    writer.writerows(yeeha)

Upvotes: 0

Views: 364

Answers (1)

Simon
Simon

Reputation: 10841

As the commenter who proposed an approach has not had the chance to outline some code for this, here's how I'd suggest doing it (edited to allow optionally signed floating point numbers with optional exponents, as suggested by an answer to Python regular expression that matches floating point numbers):

import re,sys

pat = re.compile("DV/DL += +([+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)")
values = []
for line in open("input.out","r"):
    m = pat.search(line)
    if m:
        values.append(m.group(1))
outfile = open("out.csv","w")
outfile.write(",".join(values[-2:]))

Having run this script:

$ cat out.csv
13.0462,3.7510

I haven't used the csv module in this case because it isn't really necessary for a simple output file like this. However, adding the following lines to the script will use csv to write the same data into out1.csv:

import csv

writer = csv.writer(open("out1.csv","w"))
writer.writerow(values[-2:])

Upvotes: 1

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