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A simple FASTA toolbox for small to medium size projects without dependencies.

Project description

miniFASTA

A simple FASTA toolbox for small to medium size projects without dependencies.

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FASTA files are text-based files for storing nucleotide or amino acid sequences. Reading such files is not particularly difficult, yet most off the shelf packages are overloaded with strange dependencies.

miniFASTA offers an alternative to this and brings many useful functions without relying on third party packages.

Installation

Using pip / pip3:

pip install miniFasta

Or by source:

git clone git@github.com:not-a-feature/miniFASTA.git
cd miniFASTA
pip install .

How to use

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

  • fasta_object()
    • toAmino()
    • roRevComp()
    • valid()
    • len() / str() / eq() / iter()
  • read()
  • write()
  • translate_seq()
  • reverse_comp()

fasta_object()

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

import miniFasta as mf
fo = mf.fasta_object(">Atlantic dolphin", "CGGCCTTCTATCTTCTTC", stype="DNA")
fo.getHead() or fo.head
# >Atlantic dolphin

fo.getSeq() or fo.body
# CGGCCTTCTATCTTCTTC

### Following functions are defined on a fasta_object():

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

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

# Equality 
fo == fo # True

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

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

for s in fo:
    # Iterates through the sequence of fo.

fasta_object(...).valid()

Checks if the body contains invalid characters. stype of fasta_object needs to be set in order to check for illegal characters in its body.

stype is one of:

  • ANY : [default] Allows all characters.
  • NA : Allows all Nucleic Acid Codes (DNA & RNA).
  • DNA : Allows all IUPAC DNA Codes.
  • RNA : Allows all IUPAC RNA Codes.
  • PROT: Allows all IUPAC Aminoacid Codes.

Optional: allowedChars can be set to overwrite default settings.

# The default object allows all characters.
# True
fasta_object(">valid", "Ä'_**?.asdLLA").valid()

# Only if stype is specified, valid can check for illegal characters.
# True
fasta_object(">valid", "ACGTUAGTGU", stype="NA").valid()

# False, as W is not allowed for DNA/RNA
fasta_object(">invalid", "ACWYUOTGU", stype="NA").valid() 

# True
fasta_object(">valid", "AGGATTA", stype="ANY").valid(allowedChars = "AGTC")

# True, as stype is ignored if allowedChars is set.
fasta_object(">valid", "WYU", stype="DNA").valid(allowedChars = "WYU") 

fasta_object(...).toAmino(translation_dict)

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

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

fasta_object(...).toRevComp(complement_dict)

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

fo.toRevComp() 
fo.getBody # Will return GAAGAAGATAGAAGGCCG

Reading FASTA files

read() is a fasta reader which is able to handle compressed and non-compressed files. Following compressions are supported: zip, tar, tar.gz, gz. If multiple files are stored inside an archive, all files are read. This function returns a list of fasta_objects. The entries are usually casted to upper case letters. Set read("path.fasta", upper=False) to disable casting.

fos = mf.read("dolphin.fasta") # List of fasta entries.
fos = mf.read("mouse.fasta", upper=False) # The entries won't be casted to upper case.
fos = mf.read("reads.tar.gz") # Is able to handle compressed files.

Writing FASTA files

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

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

fos = mf.read("dolphin.fasta") # List of fasta entries
mf.write(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.

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

d = {"CGG": "Z", "CTT": "A"}
mf.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.

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

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

License

Copyright (C) 2022 by Jules Kreuer - @not_a_feature
This piece of software is published unter the GNU General Public License v3.0
TLDR:

| Permissions      | Conditions                   | Limitations |
| ---------------- | ---------------------------- | ----------- |
| ✓ Commercial use | Disclose source              | ✕ Liability |
| ✓ Distribution   | License and copyright notice | ✕ Warranty  |
| ✓ Modification   | Same license                 |             |
| ✓ Patent use     | State changes                |             |
| ✓ Private use    |                              |             |

Go to LICENSE.md to see the full version.

Dependencies

In addition to packages included in Python 3, this piece of software uses 3rd-party software packages for development purposes that are not required in the published version. Go to DEPENDENCIES.md to see all dependencies and licenses.

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