tidyfasta 1.0.2

Sanitise protein FASTA files / data

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

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()