tidyfasta 1.0.5

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.

If run in non-strict mode (default), any sequence that a breaking issue, such as a non-canonical AA, dangerous characters (any non-alphanumeric character with the exception of _ -), or is just an ID without a sequence, will be ignored. If run in strict mode then an exception is raised.

When run from the command line interface the script will write a file to the same directory as the input file with the prefix tidied- followed by the input file name. If there is already an output file, then the prefix will be tidied-UNIXTIME- where UNIXTIME is the time at which the script was called.

If imported, after calling the class ProcessFasta, two member variables are available. ProcessFasta.fasta_array returns a minimally validated array of strings, where split lines are combined, excess whitespace is removed, and missing names are added. ProcessFasta.validated_array returns a validated_array of objects, where each object has two variables id and sequence. The validated array is checked for non-canonical AA in the sequence and banned characters from the ID.

Problems and fixes

Problem	Fix (Strict mode)
Sequence without ID	ID name added
Multiline sequence	One line per sequence
ID without sequence	Sequence ignored (Exception raised)
Non canonical AA	Sequence ignored (Exception raised)
Dangerous characters in ID	Sequence ignored (Exception raised)
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

$ tidyfasta --input file.txt --version

$ tidyfasta --input file.txt --help

Script

from tidyfasta.common.process import ProcessFasta

input_file = "sample.txt"

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

fasta_array = np.fasta_array
print(fasta_array)

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

np.write_fasta()