Metadata-Version: 2.1
Name: tidyfasta
Version: 1.0.3
Summary: Sanitise protein FASTA files / data
Home-page: https://github.com/maxhebditch/tidyfasta
Author: Max Hebditch
Author-email: max@maxhebditch.co.uk
License: MIT
Platform: UNKNOWN
Description-Content-Type: text/markdown

# tidyfasta

 A python program to tidy and sanitise FASTA sequence files.

 It can be imported as a package or used directly from the command line.

## Problems and fixes

| Problem                     | Fix                                     |
|-----------------------------|-----------------------------------------|
| Sequence without ID         | ID name added                           |
| ID without sequence         | Exception raised                        |
| Multiline sequence          | One line per sequence                   |
| Non canonical AA            | Exception raise                         |
| Dangerous characters in ID  | Exception raise                         |
| Lowercase AA                | Converts to uppercase AA                |
| Excessive Whitespace        | Removes excessive whitespace            | 

## Install

    pip install tidyfasta

## Usage

#### Command line interface

    $ tidyfasta --input file.txt

    $ tidyfasta --input file.txt --strict --single

#### Script

    from tidyfasta.common.process import ProcessFasta

    input_file = "sample.txt"

    np = ProcessFasta(input_file, strict=True, single=False)

    fasta_array = np.get_fasta()
    print(fasta_array)

    for i in np.validated_array:
        print(i.id+"\n")
        print(i.sequence+"\n")

    np.write_fasta()


