neatbio 0.0.2

NeatBio - a simple Yet Another BioInformatics Library for DNA Sequence

neatbio

A Simple Yet Another Bioinformatics Library for DNA,RNA and Protein Sequencing

Installation

pip install neatbio

Benefits

• Handling Sequences(DNA,RNA,Protein)
• Protein Synthesis
• Sequence Similarity
• Kmers Generation and Kmer Distance
• Probable Back Translation of Amino Acids
• Reading FASTA files

Why NeatBio?

• NeatBio is yet another bioinformatics library along side powerful and popular bioinformatics libraries such as biopython,scikit-bio,biotite.
• It is meant to complement these powerful library in a simple way.

Usage

Handling Sequences

• Neatbio offers the ability to analyse sequences for more insight

>>>import neatbio as nt
>>> seq1 = nt.Sequence('ATGCATTGA')
>>> seq1.gc
33.33333333333333
>>> seq1.gc_frequency()
3
>>> seq1.at
66.66666666666666
>>> seq1.at_frequency()
6
>>> seq1.transcribe()
'AUGCAUUGA'
>>> mrna = seq1.transcribe()
>>> nt.Sequence(mrna).back_transcribe()
'ATGCATTGA'
>>> 

>>> seq1.translate()
'MH*'
>>> seq1.translate
>>>
>>> rna_seq = nt.Sequence("AUGCAUUGA","RNA")
>>> rna_seq.seqtype
>>> Sequence(seq='AUGCAUUGA',seqtype='RNA')

Working with Proteins

>>> protein1 = nt.ProteinSeq('MIT')
>>> protein1
ProteinSeq(seq='MIT')
>>> protein1.back_translate()
'ATGATAACT'

• Note that the back_translate() function offers a probable sequence and not the exact back-translation as multiple codons can represent the same amino acids.

Convert 3 Letter Amino Acid to 1 and vice versa

>>> from neatbio.sequtils import convert_3to1,convert_1to3,get_acid_name
>>> convert_3to1('Ala')
'A'
>>> convert_1to3('L')
'Leu'

>>> get_acid_name('Ala')
'Alanine'

Generate DotPlot

>>> import neatbio as nt 
>>> import neatbio.sequtils as utils
>>> seq1 = nt.Sequence('AGTCGTACT')
>>> seq2 = nt.Sequence('AGGCGCACT')
>>> 
>>> utils.dotplot(seq1,seq2)
 |AGGCGCACT
-----------
A|■     ■  
G| ■■ ■    
T|        ■
C|   ■ ■ ■ 
G| ■■ ■    
T|        ■
A|■     ■  
C|   ■ ■ ■ 
T|        ■
>>> 

Reading FASTA Files

>>> import neatbio as nt 
>>> file1 = nt.read_fasta('sequence.fasta')
>>> file1['seqRecord']


>>> seq1 = nt.Sequence(file1['seqRecord'])

Documentation

• Please read the documentation for more information on what neatbio does and how to use is for your needs.

More Features To Add

• sequence alignment
• writing FASTA files
• support for more file formats

Acknowledgements

• Inspired by packages like BioPython,Scikit-Bio and Biotite

NB

• Contributions Are Welcomed
• Notice a bug, please let us know.
• Thanks A lot

By

• Jesse E.Agbe(JCharis)
• Jesus Saves @JCharisTech