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Data File Utils

Collection of Python scripts/utils for facilitating file manipulation tasks.

Improvements

Please see the TODO for a list of upcoming improvements.

Use Cases

Use Cases diagram

Installation

See the install instructions.

Generate shell wrapper scripts

After executing pip install data-file-utils, execute this exported script: make_executables_and_aliases.py.
This will create the wrapper shell scripts and a file containing aliases named data-file-utils-aliases.txt in the current directory.

You can then add this line to your .bashrc or .zshrc:
source dir/data-file-utils-aliases.txt
where dir is the directory that contains the aliases file.

Exported scripts

The following exported console scripts are available:

  • analyze-record-tuples
  • archive-dir
  • backup-dir
  • backup-file
  • compare-tab-files
  • create-tmp-dir
  • delete-old-files
  • find-last-directory
  • find-last-file
  • jsonl2json
  • profile-data-file
  • tsv2json
  • xlsx2tsv

analyze-record-tuples

This script will determine which records are missing from either of the two tab-delimited files. Some specified number of columns will make up the unique tuple for each line/record.

archive-dir

This script will archive the directory in-place using tar -zcvf and will apply suffix TIMESTAMP.tgz to the directory.

Sample invocation:

archive-dir /tmp/test-123/test-abc
test-abc/
test-abc/file-1
test-abc/file-2
test-abc/file-3
test-abc/file-4
Directory '/tmp/test-123/test-abc' successfully archived to 'test-abc_2024-01-02-212243.tgz'

backup-dir

This script will backup the directory in-place and will apply suffix TIMESTAMP.bak to the directory.

Sample invocation:

backup-dir /tmp/test-123                                              
Backed-up '/tmp/test-123' to '/tmp/test-123.2024-01-02-210517.bak'

backup-file

This script will backup the file in-place and will apply suffix TIMESTAMP.bak to the file.

Sample invocation:

backup-file setup.py                                                  
Backed-up 'setup.py' to 'setup.py.2024-01-02-205756.bak'

compare-tab-files

This script will parse two tab-delimited files and generate a report to indicate which lines and columns are different.

create-tmp-dir

This script will prompt the user for the following information and then create a temporary directory:

  • root directory (default is /tmp)
  • user directory (default is $USER)
  • purpose

Sample invocation:

create-tmp-dir        
Enter the root directory: [/tmp]: 
Enter the user directory: [sundaram]: 
Enter the purpose of the directory: stock-checker
Created output directory '/tmp/sundaram/stock-checker/2024-01-02-213509'

delete-old-files

This script will delete all old files belonging to the current or specified username in the /tmp or specified directory.

jsonl2json

This script will parse a JSONL file and write a JSON file for each line in the JSONL file.

profile-data-file

This script will output the following attributes of a specified file:

  • date created
  • md5sum
  • line count
  • byte size

Sample invocation:

python data_file_utils/profile_data_file.py requirements.txt
File: /home/sundaram/projects/data-file-utils/requirements.txt
md5sum: 2063352be9cbfa5bd1f1425524dbb77b
create_date: 2023-12-18 11:35:54.242520
byte_size: 14
line_count: 2

tsv2json

This script will parse a tab-delimited file and write a JSON file.

xlsx2tsv

This script will parse an Excel file and write a tab-delimited file for each worksheet.

Sample invocation:

xlsx2tsv --infile ~/projects/experiments/xlsx2tsv/genetics.xlsx 
--config_file was not specified and therefore was set to '/home/sundaram/projects/experiments/xlsx2tsv/venv/lib/python3.10/site-packages/data_file_utils/conf/config.yaml'
--outdir was not specified and therefore was set to '/tmp/xlsx2tsv/2023-12-22-142224'
Created output directory '/tmp/xlsx2tsv/2023-12-22-142224'
--logfile was not specified and therefore was set to '/tmp/xlsx2tsv/2023-12-22-142224/xlsx2tsv.log'
Sheet 'genes' has been written to '/tmp/xlsx2tsv/2023-12-22-142224/genes.tsv'
Sheet 'transcripts' has been written to '/tmp/xlsx2tsv/2023-12-22-142224/transcripts.tsv'
Sheet 'proteins' has been written to '/tmp/xlsx2tsv/2023-12-22-142224/proteins.tsv'
The log file is '/tmp/xlsx2tsv/2023-12-22-142224/xlsx2tsv.log'
Execution of '/home/sundaram/projects/experiments/xlsx2tsv/venv/lib/python3.10/site-packages/data_file_utils/xlsx2tsv.py' completed

Contributing

Pull requests are welcome.
For major changes, please open an issue first to discuss what you would like to change.

To-Do/Coming Next

Please view the listing of planned improvements here.

CHANGELOG

Please view the CHANGELOG here.

License

GNU AFFERO GENERAL PUBLIC LICENSE