miniFASTA

An easy FASTA object handler, reader, writer and translator for small to medium size projects without dependencies.

Installation

Using pip / pip3:

pip install miniFasta

Or by source:

git clone [email protected]:not-a-feature/miniFASTA.git
cd miniFASTA
pip3 install .

How to use

miniFASTA offers easy to use functions for fasta handling. The five main parts are:

• fasta_object()
• read_fasta()
• write_fasta()
• translate_seq()
• reverse_comp()

fasta_object()

The core component of miniFASTA is the fasta_object(). This object represents an entry in a FASTA file and consists of a head and body.

from miniFasta import miniFasta as fasta
fo = fasta.fasta_object(">Atlantic dolphin", "CGGCCTTCTATCTTCTTC")
print(fo.head) # >Atlantic dolphin
print(fo.body) # CGGCCTTCTATCTTCTTC

Following functions are defined on a fasta_object():

str()

str(fo) # will return:
# >Atlantic dolphin
# CGGCCTTCTATCTTCTTC

len()

len(fo) # will return 18, the length of the body

==

print(fo == fo) # True

fo_b = fasta.fasta_object(">Same Body", "CGGCCTTCTATCTTCTTC")
print(fo == fo_b) # True

fo_c = fasta.fasta_object(">Different Body", "ZZZZAGCTAG")
print(fo == fo_c) # False

toAmino(translation_dict)

Translates the body to an amino-acid sequence. See tranlate_seq() for more details.

fo.toAmino() 
print(fo.body) # Will return RPSIFF
d = {"CCG": "Z", "CTT": "A" ...}
fo.toAmino(d) 
print(fo.body) # Will return ZA...

toRevComp(complement_dict)

Converts the body to its reverse comlement. See reverse_comp() for more details.

fo.toRevComp() 
print(fo.body) # Will return GAAGAAGATAGAAGGCCG

Reading FASTA files

read_fasta() is a basic fasta reader. It reads a fasta-style file and returns a list of fasta_objects. The entries are usually casted to upper case letters. Set read_fasta("path.fasta", upper=False) to disable casting.

fos = fasta.read_fasta("dolphin.fasta") # List of fasta entries
fos = fasta.read_fasta("cat.fasta", upper=False)

Writing FASTA files

write_fasta() is a basic fasta reader. It takes a single or a list of fasta_objects and writes it to the given path.

The file is usually overwritten. Set write_fasta(fo, "path.fasta", mode="a") to append file.

fos = fasta.read_fasta("dolphin.fasta") # List of fasta entries
fasta.write_fasta(fos, "new.fasta")

Sequence translation

translate_seq() translates a sequence starting at position 0. Unless translation_dict is provided, the standart bacterial code is used. If the codon was not found, it will be replaced by an ~. Tailing bases that do not fit into a codon will be ignored.

fasta.translate_seq("CGGCCTTCTATCTTCTTC") # Will return RPSIFF

d = {"CGG": "Z", "CTT": "A"}
fasta.translate_seq("CGGCTT", d) # Will return ZA.

Reverse Complement

reverse_comp() converts a sequence to its reverse comlement. Unless complement_dict is provided, the standart complement is used. If no complement was found, the nucleotide remains unchanged.

fasta.reverse_comp("CGGCCTTCTATCTTCTTC") # Will return GAAGAAGATAGAAGGCCG

d = {"C": "Z", "T": "Y"}
fasta.reverse_comp("TC", d) # Will return ZY