dna-ibp 1.1.0

Command-line tool for DNA sequence analysis and processing

DNA IBP Command Line Interface

CLI application for the DNA analyser IBP API wrapper (https://github.com/patrikkaura/dna-analyser-ibp)

Installation requirements

• Python v.3.10 or better
• pip

Installation guide

Run the following command in your command line

pip install dna-ibp

Command list

Upon entering any command prefaced by `dna-ibp`, the user is prompted to enter their DNA analyser (https://bioinformatics.ibp.cz/) credentials.

C:\Users\kryst>dna-ibp sequence show all
Enter your email        [e-mail]
Enter your password
2025-07-31 13:03:51.383532 [INFO]: User [e-mail] is trying to login ...
2025-07-31 13:03:51.612553 [INFO]: User [e-mail] is successfully loged in ...

This login session lasts for 60 minutes or can be disconnected prematurely by using the --reset/-r command:

C:\Users\kryst>dna-ibp --reset
2025-07-31 13:07:26.229684 [INFO]: User [e-mail] logged out...

The --help/-h command can be used after any previous command to list possible sub-commands or arguments:

C:\Users\kryst>dna-ibp sequence --help
usage: dna-ibp sequence [-h] {create,show,data,delete,count} ...

positional arguments:
  {create,show,data,delete,count}
    create              Parser for uploading sequences to your DNA analyser.
    show                Load sequence(s) uploaded in your DNA analyser account.
    delete              Delete chosen sequence(s) from your DNA analyser account.
    count               Recount nucleotides for a given sequence.

options:
  -h, --help            show this help message and exit

Sequence

Create

Uploading sequences on your DNA analyser account is done via the `dna-ibp create` command. Possible arguments are:

--file FILE, -f FILE  Upload a sequence by providing path to a file (.txt of FASTA)
--id ID, -i ID        Upload a sequence via NCBI ID.
--text TEXT, -t TEXT  Upload a sequence via pasting a string.
--circular, --no-circular
                      Specify whether the sequence is circular or not (--circular or --no-circular). (default: True)
--tags [TAGS ...]     (OPTIONAL) Specify tags associated with the uploaded sequence.
--nucleic {DNA,RNA}   Specify whether the sequence nucleic type (choices: DNA, RNA, default val: DNA).
--name NAME, -n NAME  Specify name of the uploaded sequence.

Show

Listing all uploaded sequences on your DNA analyser account is done via the `dna-ibp show` command. Possible arguments are:

positional arguments:
  sequence       Sequence to be processed by related methods.