- Untar a Tar.gz File with Ease Using Python: Tips and Tricks
- What is a Tar.gz File?
- Python’s Tarfile Module
- Untarring a Tar.gz File
- Extracting Specific Files
- Extracting to a Different Directory
- Conclusion
- How to decompress and untar tar files
- How to Decompress a TAR file into TXT (read a CEL file) in either Python or R
- Uncompress tar file hierarchy on AWS S3 using CLI?
- How to untar file in memory (c programming)?
- Распаковка файлов из архивов zip или tar.gz с помощью Python
- Шаг 1: получить информацию из архива zip или tar.gz
- Шаг 2: перечислить и прочитать все файлы из архива
- Шаг 3: извлечь файлы из zip-архива
- Шаг 4: извлечь файлы из tar/tar.gz
- Шаг 5: извлечь один файл из архива
- Заключение
Untar a Tar.gz File with Ease Using Python: Tips and Tricks
If you’re working with compressed files in your Python project, you may encounter tar.gz files. Tar.gz files are a common way to compress and bundle multiple files into a single archive. In this article, we’ll explore some tips and tricks for untarring a tar.gz file with ease using Python.
What is a Tar.gz File?
A tar.gz file is a compressed archive file that combines the functionality of a tar file and gzip compression. A tar file is an archive format for Unix-based systems that bundles multiple files into a single file. Gzip is a file compression utility that reduces the size of a file without losing any data. When combined, tar.gz files compress multiple files into a smaller, single file that is easier to handle.
Python’s Tarfile Module
Python’s built-in tarfile module makes it easy to work with tar files of all kinds. The tarfile module provides functions for creating, reading, and extracting tar archives. It also supports gzip compression, which makes it ideal for working with tar.gz files.
Untarring a Tar.gz File
To untar a tar.gz file, you can use the tarfile module’s extractall() function. This function extracts all the files from the archive to the current working directory. Here’s some code to get you started:
import tarfile # Open the tar.gz file tar = tarfile.open("example.tar.gz", "r:gz") # Extract all the files to the current working directory tar.extractall() # Close the tar.gz file tar.close() This code opens the example.tar.gz file, extracts all the files to the current working directory, and then closes the file. Note that the «r:gz» argument passed to the open() function tells the tarfile module that the file is a tar.gz file and should be handled as such.
Extracting Specific Files
If you only want to extract specific files from the archive, you can use the extract() function instead of extractall(). The extract() function takes a single argument, which is the name of the file you want to extract. Here’s an example:
import tarfile # Open the tar.gz file tar = tarfile.open("example.tar.gz", "r:gz") # Extract a specific file tar.extract("example.txt") # Close the tar.gz file tar.close() This code opens the example.tar.gz file, extracts the example.txt file to the current working directory, and then closes the file.
Extracting to a Different Directory
By default, the extractall() and extract() functions extract files to the current working directory. However, you can specify a different directory by passing a path argument to the functions. Here’s an example:
import tarfile # Open the tar.gz file tar = tarfile.open("example.tar.gz", "r:gz") # Extract all the files to a different directory tar.extractall("path/to/directory") # Close the tar.gz file tar.close() This code opens the example.tar.gz file, extracts all the files to the «path/to/directory» directory, and then closes the file.
Conclusion
Working with tar.gz files in Python is easy and straightforward using the tarfile module. With just a few lines of code, you can extract all the files from an archive, extract specific files, or extract files to a different directory. Hopefully, these tips and tricks will help you work with tar.gz files more efficiently in your Python projects.
How to decompress and untar tar files
Tar files were originally (IIRC 🙂 ) created for tape based storage, so their contents can be streamed, therefore you can simply pipe the output of the decompression algorithm into tar via stdout/stdin For 7zip you could use: This will write the contents of the file into the current directory and echo the filenames as it’s going. For gzip/bzip you can just use tar as it has plugins already built in for these (I couldn’t see one for 7zip) will extract a gzipped file will extract a bzip2’d tar file Those are the most common Solution: S3 isn’t going to uncompress files for you.
How to Decompress a TAR file into TXT (read a CEL file) in either Python or R
Backgound Research
So I’ve been working on it around an hour — here are the results.
The file that you are trying to open is GSM2458563_Control_1_0 is compressed inside .gz file, which contains a .CELL file, therefore it’s unreadable.
Such files are published by the «National Center for Biotechnology Information».
Seen a Python 2 code to open them:
from Bio.Affy import CelFile with open('GSM2458563_Control_1_0.CEL') as file: c = CelFile.read(file) I’ve found documentation about Bio.Affy on version 1.74 of biopython.
Yet current biopython readme says:
«. Biopython 1.76 was our final release to support Python 2.7 and Python 3.5.»
Nowadays Python 2 is deprecated, not to mention that the library mentioned above has evolved and changed tremendously.
So I found another way around it, using R.
Operation System : Windows 64 RStudio : Version 1.3.1073 R Version : R-4.0.2 for Windows I’ve pre-installed the dependencies mentioned below.
Use the GEOquery.getGEO function to fetch from NCBI GEO the file.
# Presequites # Download and install Rtools custom from http://cran.r-project.org/bin/windows/Rtools/ # Install BiocManager if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("GEOquery") library(GEOquery) # Download and open the data gse Unzip and Untar Those tar.gz or tar.bz2 Files in One Step, To gunzip and untar a file in a single step, use the following—note that the z switch is the important one that tells tar to unzip it. tar xvfz somefilename.tar.gz To use bunzip2 to extract your tar.bz2 file in a single step, use the j switch instead. tar xvfj somefilename.tar.bz2 Ahh, nice and simple, just the …
How do I uncompress a quite big tar file which is 200GB larger much than memory?
If you have an archive that is compressed, you don't need to uncompress it on disk before extracting the files. Tar files were originally (IIRC 🙂 ) created for tape based storage, so their contents can be streamed, therefore you can simply pipe the output of the decompression algorithm into tar via stdout/stdin
7z x -so wikipedia-en-html.tar.7z | tar xv This will write the contents of the file into the current directory and echo the filenames as it's going. If you don't want to see the files as it's going simply remove the 'v' from tar.
The switches to 7zip tell it to e'x'tract and -so tells it to use StOut instead of writing to disk.
For gzip/bzip you can just use tar as it has plugins already built in for these (I couldn't see one for 7zip)
will extract a gzipped file
will extract a bzip2'd tar file
Those are the most common
Linux - How can I untar a tar.bz file in unix?, 3 Answers. use the -j option of tar. I think it is preferred to leave the - off. Just tar xjf /path/to/archive.tar.bz is enough. If the file does not end in one of the recognised endings, .bz2, .bz, .tbz2 or .tbz, bzip2 complains that it cannot guess the name of the original file, and uses the original name with .out appended. …
Uncompress tar file hierarchy on AWS S3 using CLI?
S3 isn't going to uncompress files for you. You have to push the files to S3 in the state you want S3 to store them in. The aws s3 sync command (or a similar tool that does incremental updates based on the MD5 hash) is going to be your best option. You could probably split up the sync command into multiple, parallel sync commands. Perhaps run one process per subdirectory.
Regarding your comment that aws s3 sync "may take a long time to pump millions of files across the pipe", you should zip up the files and push them to an EC2 server first if you aren't already doing this on EC2. You should be using an EC2 server in the same region as the S3 bucket, an instance type with 10Gbps network performance, and the EC2 server should have Enhanced Networking enabled. This will give you the fastest possible connection to S3.
Net - Decompress tar files using C#, there are 2 ways to compress/decompress in .net first you can use gzipstream class and deflatstream both can actually do compress your files in .gz format so if you compressed any file in gzipstream it can be opened with any popular compression applications such as winzip/ winrar, 7zip but you can't …
How to untar file in memory (c programming)?
I suspect that libtar is the answer.
Using libtar, you can specify your own functions for opening/closing, reading and writing. From the manpage:
int tar_open(TAR **t, char *pathname, tartype_t *type, int oflags, int mode, int options); The tar_open() function opens a tar archive file corresponding to the filename named by the pathname argument. The oflags argument must be either O_RDONLY or O_WRONLY .
The type argument specifies the access methods for the given file type. The tartype_t structure has members named openfunc() , closefunc() , readfunc() and writefunc() , which are pointers to the functions for opening, closing, reading, and writing the file, respectively. If type is NULL , the file type defaults to a normal file, and the standard open() , close() , read() , and write() functions are used.
I made an example, how to read file contents from an in-memory tar. The is_file_in_tar() function returns the length and the start ing position of the name d file if it is stored in the tar :
#include #include #include #include struct tar < char name[100]; char _unused[24]; char size[12]; char _padding[376]; >*tar; int is_file_in_tar( struct tar *tar, char *name, char **start, int *length )< for( ; tar->name[0]; tar+=1+(*length+511)/512 )< sscanf( tar->size, "%o", length); if( !strcmp(tar->name,name) ) < *start = (char*)(tar+1); return 1; >> return 0; > int main() < int fd=open( "libtar-1.2.11.tar", O_RDONLY ); tar=mmap(NULL, 808960, PROT_READ, MAP_PRIVATE, fd, 0); char *start; int length; char name[]="libtar-1.2.11/TODO"; if( is_file_in_tar(tar,name,&start,&length) ) printf("%.*s",length,start); >You can execute tar utility redirected to stdout. ( tar --to-stdout ). You should run it using forkpty() or popen() in order to read the output.
Tar - how to untar file in memory (c programming)?, int tar_open (TAR **t, char *pathname, tartype_t *type, int oflags, int mode, int options); The tar_open () function opens a tar archive file corresponding to the filename named by the pathname argument. The oflags argument must be either O_RDONLY or O_WRONLY. The type argument specifies the access …
Распаковка файлов из архивов zip или tar.gz с помощью Python
Из этой статьи вы узнаете, как распаковать один или несколько архивов zip и tar.gz и получить информацию о них средствами языка Python. Мы рассмотрим извлечение одного или нескольких файлов из архива.
Шаг 1: получить информацию из архива zip или tar.gz
Сперва мы просмотрим содержимое zip-файла с помощью этого фрагмента кода:
from zipfile import ZipFile zipfile = 'file.zip' z = ZipFile(zipfile) z.infolist()
Таким образом мы сможем узнать размеры и имена двух файлов:
Шаг 2: перечислить и прочитать все файлы из архива
Теперь мы можем получить список всех файлов в архиве:
from zipfile import ZipFile archive = 'file.zip' zip_file = ZipFile(archive) [text_file.filename for text_file in zip_file.infolist() ]
['pandas-dataframe-background-color-based-condition-value-python.png', 'text1.txt']
Если вам нужно отсортировать файлы – например, получить только json – или прочитать их в формате датафреймов Pandas, можно сделать это следующим образом:
from zipfile import ZipFile archive = 'file.zip' zip_file = ZipFile(archive) dfs = dfs
Шаг 3: извлечь файлы из zip-архива
Пакет zipfile можно использовать для извлечения файлов из zip-архивов. Базовый пример:
import zipfile archive = 'file.zip' with zipfile.ZipFile(archive, 'r') as zip_file: zip_file.extractall(directory_to_extract_to)
Шаг 4: извлечь файлы из tar/tar.gz
Чтобы извлечь файлы из архивов tar/tar.gz , можно воспользоваться кодом, приведенным ниже. Он использует модуль tarfile и разделяет эти два типа, чтобы применить подходящий режим распаковки:
import tarfile zipfile = 'file.zip' if zipfile.endswith("tar.gz"): tar = tarfile.open(zipfile, "r:gz") elif zipfile.endswith("tar"): tar = tarfile.open(zipfile, "r:") tar.extractall() tar.close() Примечание: все файлы из архива будут распакованы в текущей для данного скрипта рабочей директории.
Шаг 5: извлечь один файл из архива
Если вам нужно получить только один файл из архива, можно использовать метод zipObject.extract(fileName, 'temp_py') . Простой пример:
import zipfile archive = 'file.zip' with zipfile.ZipFile(archive, 'r') as zip_file: zip_file.extract('text1.txt', '.') В этом примере мы извлечём файл 'text1.txt' в текущую рабочую директорию. Если вам нужно извлечь файл в другую директорию, можете изменить второй параметр — '.'
Заключение
В этом уроке мы выяснили, как с помощью Python извлечь один или несколько файлов из различных архивов, а также — как вывести список запакованных файлов и получить из них информацию. Мы затронули работу с двумя пакетами: zipfile и tarfile.