Question

I am using the script below to extract data from some trajectory file and dump the data into new files files. I can use directive “>” to redirect results into a file but I need to do like this for more then 2000 files then. For make things easy I tried to open a file and let the python itself direct the results into a file.

To achieve that I added a line, at the place, (##) in the code, to open a file as shown below.
Also I added a line to direct the results into a file as shown in the code below at line contains (###).

#!/usr/bin/env python
'''
always put -- #!/usr/bin/env python -- at the shebang
'''

from Scientific.IO.NetCDF import NetCDFFile as Dataset
import itertools as itx


inputfile = "../traj-waters/waters1445-MD001-run1000.traj"


for FRAMES in range(0,2):
   frame = FRAMES

   text_file = open("velo-Output.dat", "w")   (##)

   #inputfile = 'mdcrd'
   ppp = inputfile

   def grouper(n, iterable, fillvalue=None):
       args = [iter(iterable)] * n
       return itx.izip_longest(fillvalue=fillvalue, *args)

   formatxyz = "%12.7f%12.7f%12.7f%12.7f%12.7f%12.7f"
   formatxyz_size = 6
   formatxyzshort = "%12.7f%12.7f%12.7f"
   formatxyzshort_size = 3

   #ncfile = Dataset(inpitfile, 'r')
   ncfile = Dataset(ppp, 'r')

   variableNames = ncfile.variables.keys()
   #print variableNames

   shape = ncfile.variables['coordinates'].shape
   '''
   do the header
   '''

   print 'title ' + str(frame)
   print "%5i%15.7e" % (shape[1],ncfile.variables['time'][frame])


   '''
   do the velocities
   '''
   try:
       xyz = ncfile.variables['velocities'][frame]
       temp = grouper(2, xyz, "")

       for i in temp:
           z = tuple(itx.chain(*i))
           if (len(z) == formatxyz_size): 
               print formatxyz % z
               text_file.write('formatxyz\n' % z))  (###)
           elif (len(z) == formatxyzshort_size): print formatxyzshort % z


   except(KeyError):

       xyz = [0] * shape[2] 
       xyz = [xyz] * shape[1]
       temp = grouper(2, xyz, "")

       for i in temp:
           z = tuple(itx.chain(*i))
           if (len(z) == formatxyz_size): print formatxyz % z
           elif (len(z) == formatxyzshort_size): print formatxyzshort % z
           x = ncfile.variables['cell_angles'][frame]
           y = ncfile.variables['cell_lengths'][frame]
   text_file.close()

But I get error if I run this code as below.

  Traceback (most recent call last):
File "./Nctorst-onlyVelo.py", line 73, in <module>
  text_file.write(str('formatxyz\n' % z))
TypeError: not all arguments converted during string formatting

Since I am newbie into python I find lost to correct this issue.

Advance thanks for help.
Regards

Answer 1

Either you made a Typo, or did not understand how string formating with replacement operator works

The Line

text_file.write('formatxyz\n' % z))  (###)

Should be written similar to the previous line

text_file.write(formatxyz % z + '\n')  (###)

Also you should look forward to use the Format String Syntax