Metadata-Version: 2.3
Name: dna-ibp
Version: 1.1.0
Summary: Command-line tool for DNA sequence analysis and processing
License: MIT
Keywords: bioinformatics,DNA,cli
Author: Kryštof Kotrys
Author-email: krystofkotrys@gmail.com
Requires-Python: >=3.10,<4.0
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Dist: DNA_analyser_IBP (>=3.7.1)
Project-URL: Homepage, https://github.com/krystofkotrys/dna-ibp-cli
Description-Content-Type: text/markdown

<h1 align='center'> DNA IBP Command Line Interface </h1>
CLI application for the DNA analyser IBP API wrapper (https://github.com/patrikkaura/dna-analyser-ibp)

<h2>Installation requirements</h2>

* Python v.3.10 or better
* pip

<h2>Installation guide</h2>

Run the following command in your command line

```command line
pip install dna-ibp
```

<h2>Command list</h2>
Upon entering any command prefaced by `dna-ibp`, the user is prompted to enter their DNA analyser (https://bioinformatics.ibp.cz/) credentials.

```command line
C:\Users\kryst>dna-ibp sequence show all
Enter your email        217346@vutbr.cz
Enter your password
2025-07-31 13:03:51.383532 [INFO]: User 217346@vutbr.cz is trying to login ...
2025-07-31 13:03:51.612553 [INFO]: User 217346@vutbr.cz is successfully loged in ...
```
This login session lasts for 60 minutes or can be disconnected prematurely by using the `--reset`/`-r` command:

```command line
C:\Users\kryst>dna-ibp --reset
2025-07-31 13:07:26.229684 [INFO]: User 217346@vutbr.cz logged out...
```

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

```command line
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
```

<h3>Sequence</h3>
<h5>Create</h5>
Uploading sequences on your DNA analyser account is done via the `dna-ibp create` command. Possible arguments are:

```command line
--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.
```

<h5>Show</h5>
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.
```

