Question

I’m new to Python, and I need to do a parsing exercise. I got a file, and I need to parse it (just the headers), but after the process, i need to keep the file the same format, the same extension, and at the same place in disk, but only with the differences of new headers..

I tried this code…

for line in open ('/home/name/db/str/dir/numbers/str.phy'):
    if line.startswith('ENS'):
        linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
        print linepars

..and it does the job, but I don’t know how to “overwrite” the file with the new parsing.

Answer 1

The easiest way, but not the most efficient (by far, and especially for long files) would be to rewrite the complete file.

You could do this by opening a second file handle and rewriting each line, except in the case of the header, you’d write the parsed header. For example,

fr = open('/home/name/db/str/dir/numbers/str.phy')
fw = open('/home/name/db/str/dir/numbers/str.phy.parsed', 'w') # Name this whatever makes sense

for line in fr:
    if line.startswith('ENS'):
        linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
        fw.write(linepars)
    else:
        fw.write(line)

fw.close()
fr.close()

EDIT: Note that this does not use readlines(), so its more memory efficient. It also does not store every output line, but only one at a time, writing it to file immediately.

Just as a cool trick, you could use the with statement on the input file to avoid having to close it (Python 2.5+):

fw = open('/home/name/db/str/dir/numbers/str.phy.parsed', 'w') # Name this whatever makes sense

with open('/home/name/db/str/dir/numbers/str.phy') as fr:
    for line in fr:
        if line.startswith('ENS'):
            linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
            fw.write(linepars)
        else:
             fw.write(line)

fw.close()

P.S. Welcome 🙂