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

Overview

miniFASTA

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

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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.

Atlantic dolphin", "CGGCCTTCTATCTTCTTC") print(fo.head) # >Atlantic dolphin print(fo.body) # CGGCCTTCTATCTTCTTC">
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

==

Same Body", "CGGCCTTCTATCTTCTTC") print(fo == fo_b) # True fo_c = fasta.fasta_object(">Different Body", "ZZZZAGCTAG") print(fo == fo_c) # False">
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
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Comments
Releases(v3.0.2)
  • v3.0.2(Nov 8, 2022)

    What's Changed

    • Add support of py3.11 and update gh actions by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/22

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v3.0.1...v3.0.2

    Source code(tar.gz)
    Source code(zip)
  • v3.0.1(Oct 12, 2022)

    What's Changed

    • Update README.md by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/18
    • Merge by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/19
    • switch to iterator by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/20
    • Add dataclass decorator by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/21

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v2.4.1...v3.0.1

    Source code(tar.gz)
    Source code(zip)
  • v2.4.1(Sep 24, 2022)

    What's Changed

    • add py3.7 support by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/17

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v2.4.0...v2.4.1

    Source code(tar.gz)
    Source code(zip)
  • v2.4.0(Jul 4, 2022)

    What's Changed

    • Update README.md by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/15
    • add option to read only the body by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/16

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v2.3.2...v2.4.0

    Source code(tar.gz)
    Source code(zip)
  • v2.3.2(Mar 11, 2022)

    What's Changed

    • Black code formatting by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/14

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v2.3.1...v2.3.2

    Source code(tar.gz)
    Source code(zip)
  • v2.3.1(Feb 23, 2022)

    What's Changed

    • Add type information and update readme by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/13

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v2.3.0...v2.3.1

    Source code(tar.gz)
    Source code(zip)
  • v2.3.0(Feb 23, 2022)

    What's Changed

    • Dev by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/11
    • add iter and getter methods by @not-a-feature in https://github.com/not-a-feature/miniFASTA/pull/12

    Full Changelog: https://github.com/not-a-feature/miniFASTA/compare/v2.2.1...v2.3.0

    Source code(tar.gz)
    Source code(zip)
Owner
Jules Kreuer
Jules Kreuer
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