Home » Replace string in a huge (70GB), one line, text file

Replace string in a huge (70GB), one line, text file

Solutons:


For such a big file, one possibility is Flex. Let unk.l be:

%%
<unk>     printf("<raw_unk>");  
%%

Then compile and execute:

$ flex -o unk.c  unk.l
$ cc -o unk -O2 unk.c -lfl
$ unk < corpus.txt > corpus.txt.new

The usual text processing tools are not designed to handle lines that don’t fit in RAM. They tend to work by reading one record (one line), manipulating it, and outputting the result, then proceeding to the next record (line).

If there’s an ASCII character that appears frequently in the file and doesn’t appear in <unk> or <raw_unk>, then you can use that as the record separator. Since most tools don’t allow custom record separators, swap between that character and newlines. tr processes bytes, not lines, so it doesn’t care about any record size. Supposing that ; works:

<corpus.txt tr 'n;' ';n' |
sed 's/<unk>/<raw_unk>/g' |
tr 'n;' ';n' >corpus.txt.new

You could also anchor on the first character of the text you’re searching for, assuming that it isn’t repeated in the search text and it appears frequently enough. If the file may start with unk>, change the sed command to sed '2,$ s/… to avoid a spurious match.

<corpus.txt tr 'n<' '<n' |
sed 's/^unk>/raw_unk>/g' |
tr 'n<' '<n' >corpus.txt.new

Alternatively, use the last character.

<corpus.txt tr 'n>' '>n' |
sed 's/<unk$/<raw_unk/g' |
tr 'n>' '>n' >corpus.txt.new

Note that this technique assumes that sed operates seamlessly on a file that doesn’t end with a newline, i.e. that it processes the last partial line without truncating it and without appending a final newline. It works with GNU sed. If you can pick the last character of the file as the record separator, you’ll avoid any portability trouble.

So you don’t have enough physical memory (RAM) to hold the whole file at once, but on a 64-bit system you have enough virtual address space to map the entire file. Virtual mappings can be useful as a simple hack in cases like this.

The necessary operations are all included in Python. There are several annoying subtleties, but it does avoid having to write C code. In particular, care is needed to avoid copying the file in memory, which would defeat the point entirely. On the plus side, you get error-reporting for free (python “exceptions”) :).

#!/usr/bin/python3
# This script takes input from stdin
# (but it must be a regular file, to support mapping it),
# and writes the result to stdout.

search = b'<unk>'
replace = b'<raw_unk>'


import sys
import os
import mmap

# sys.stdout requires str, but we want to write bytes
out_bytes = sys.stdout.buffer

mem = mmap.mmap(sys.stdin.fileno(), 0, access=mmap.ACCESS_READ)
i = mem.find(search)
if i < 0:
    sys.exit("Search string not found")

# mmap object subscripts to bytes (making a copy)
# memoryview object subscripts to a memoryview object
# (it implements the buffer protocol).
view = memoryview(mem)

out_bytes.write(view[:i])
out_bytes.write(replace)
out_bytes.write(view[i+len(search):])

Related Solutions

Joining bash arguments into single string with spaces

[*] I believe that this does what you want. It will put all the arguments in one string, separated by spaces, with single quotes around all: str="'$*'" $* produces all the scripts arguments separated by the first character of $IFS which, by default, is a space....

AddTransient, AddScoped and AddSingleton Services Differences

TL;DR Transient objects are always different; a new instance is provided to every controller and every service. Scoped objects are the same within a request, but different across different requests. Singleton objects are the same for every object and every...

How to download package not install it with apt-get command?

Use --download-only: sudo apt-get install --download-only pppoe This will download pppoe and any dependencies you need, and place them in /var/cache/apt/archives. That way a subsequent apt-get install pppoe will be able to complete without any extra downloads....

What defines the maximum size for a command single argument?

Answers Definitely not a bug. The parameter which defines the maximum size for one argument is MAX_ARG_STRLEN. There is no documentation for this parameter other than the comments in binfmts.h: /* * These are the maximum length and maximum number of strings...

Bulk rename, change prefix

I'd say the simplest it to just use the rename command which is common on many Linux distributions. There are two common versions of this command so check its man page to find which one you have: ## rename from Perl (common in Debian systems -- Ubuntu, Mint,...

Output from ls has newlines but displays on a single line. Why?

When you pipe the output, ls acts differently. This fact is hidden away in the info documentation: If standard output is a terminal, the output is in columns (sorted vertically) and control characters are output as question marks; otherwise, the output is...

mv: Move file only if destination does not exist

mv -vn file1 file2. This command will do what you want. You can skip -v if you want. -v makes it verbose - mv will tell you that it moved file if it moves it(useful, since there is possibility that file will not be moved) -n moves only if file2 does not exist....

Is it possible to store and query JSON in SQLite?

SQLite 3.9 introduced a new extension (JSON1) that allows you to easily work with JSON data . Also, it introduced support for indexes on expressions, which (in my understanding) should allow you to define indexes on your JSON data as well. PostgreSQL has some...

Combining tail && journalctl

You could use: journalctl -u service-name -f -f, --follow Show only the most recent journal entries, and continuously print new entries as they are appended to the journal. Here I've added "service-name" to distinguish this answer from others; you substitute...

how can shellshock be exploited over SSH?

One example where this can be exploited is on servers with an authorized_keys forced command. When adding an entry to ~/.ssh/authorized_keys, you can prefix the line with command="foo" to force foo to be run any time that ssh public key is used. With this...

Why doesn’t the tilde (~) expand inside double quotes?

The reason, because inside double quotes, tilde ~ has no special meaning, it's treated as literal. POSIX defines Double-Quotes as: Enclosing characters in double-quotes ( "" ) shall preserve the literal value of all characters within the double-quotes, with the...

What is GNU Info for?

GNU Info was designed to offer documentation that was comprehensive, hyperlinked, and possible to output to multiple formats. Man pages were available, and they were great at providing printed output. However, they were designed such that each man page had a...

Set systemd service to execute after fstab mount

a CIFS network location is mounted via /etc/fstab to /mnt/ on boot-up. No, it is not. Get this right, and the rest falls into place naturally. The mount is handled by a (generated) systemd mount unit that will be named something like mnt-wibble.mount. You can...

Merge two video clips into one, placing them next to each other

To be honest, using the accepted answer resulted in a lot of dropped frames for me. However, using the hstack filter_complex produced perfectly fluid output: ffmpeg -i left.mp4 -i right.mp4 -filter_complex hstack output.mp4 ffmpeg -i input1.mp4 -i input2.mp4...

How portable are /dev/stdin, /dev/stdout and /dev/stderr?

It's been available on Linux back into its prehistory. It is not POSIX, although many actual shells (including AT&T ksh and bash) will simulate it if it's not present in the OS; note that this simulation only works at the shell level (i.e. redirection or...

How can I increase the number of inodes in an ext4 filesystem?

It seems that you have a lot more files than normal expectation. I don't know whether there is a solution to change the inode table size dynamically. I'm afraid that you need to back-up your data, and create new filesystem, and restore your data. To create new...

Why doesn’t cp have a progress bar like wget?

The tradition in unix tools is to display messages only if something goes wrong. I think this is both for design and practical reasons. The design is intended to make it obvious when something goes wrong: you get an error message, and it's not drowned in...