pyoinformatics 0.2.5

A simple bioinformatics package

pyoinformatics 🐍

pip install pyoinformatics

Examples

Find the reverse complement of all the sequences in a file:

import pyoinformatics as pyo

with open('out.fasta', 'w') as f:
  for seq in pyo.read_fasta('in.fasta'):
    f.writelines(seq.reverse_complement().to_fasta())

Count the number of occurrences of 'ATG' in seq object

seq.count('ATG')

Count the number of occurrences of 'ATG' in seq object that differ by <= 1 base.

seq.count('ATG', 1)

Find the average position of all occurrences of 'ATG' in a fasta file

from statistics import mean
for seq in pyo.read_fasta('in.fasta'):
  print(mean(seq.find('ATG')))

Find the number of occurrences of 'ATG' or 'AAG' in seq object

len(seq1.find('A[AT]G'))

ASCI plot the relative nt counts for all the sequences in a file

for seq in pyo.read_fasta('in.fasta'):
  counts = seq.counts
  print(f">{seq.id}")
  for nt in sorted(counts.keys()):
    bar = int((counts[nt]/len(seq))*100)
    print(f"{nt}: {'◊' * bar}")

>HSBGPG Human gene for bone gla protein (BGP)
A: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
C: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
G: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
T: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
>HSGLTH1 Human theta 1-globin gene
A: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊
C: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
G: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
T: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊