simple file flow question with csv.reader

[Tim Chase]

On 11/02/11 16:13, Matt wrote:
> Hi All,
>
> I am trying to do a really simple file operation, yet, it befuddles me...
>
> I have a few hundred .csv files, and to each file, I want to manipulate the data, then save back to the original file. The code below will open up the files, and do the proper manipulations-- but I can't seem to save the files after the manipulation..
>
> How can I save the files-- or do I need to try something else maybe with split, join, etc..
>
>
> import os
> import csv
> for filename in os.listdir("/home/matthew/Desktop/pero.ngs/blast"):
> 	with open(filename, 'rw') as f:
> 		reader = csv.reader(f)
> 		for row in reader:
> 			print ">",row[0],row[4],"\n",row[1], "\n",">", row[2], "\n", row[3]

Your last line just prints the data to standard-out.  You can 
either pipe the output to a file:

   python myprog.py > output.txt

or you can write them to a single output file:

   out = file('output.txt', 'w')
   for filename in os.listdir(...):
     with open(filename, 'rw') as f:
       reader = csv.reader(f)
       for row in reader:
         out.write(">%s%s\n%s\n>%s\n>%s\n%s" % (
           row[0], row[4], row[1], row[2], row[3]))

or you can write them to output files on a per-input basis:

   for filename in os.listdir(SOURCE_LOC):
     with open(filename, 'r') as f:
       outname = os.path.join(
         DEST_LOC,
         os.path.basename(filename),
         )
       with file(outname, 'wb') as out:
         for row in reader:
           out.write(">%s%s\n%s\n>%s\n>%s\n%s" % (
             row[0], row[4], row[1], row[2], row[3]))

-tkc