A simple bioinformatics package
Project description
pyoinformatics ๐
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}: {'โ' * bar}")
>HSBGPG Human gene for bone gla protein (BGP)
A: โโโโโโโโโโโโโโโโโ
C: โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
G: โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
T: โโโโโโโโโโโโโโโโโโ
>HSGLTH1 Human theta 1-globin gene
A: โโโโโโโโโโโโโโ
C: โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
G: โโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโโ
T: โโโโโโโโโโโโโโโ
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
pyoinformatics-0.2.3.tar.gz
(5.0 kB
view hashes)
Built Distribution
Close
Hashes for pyoinformatics-0.2.3-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 7d739c9486c2e298220227d0882e453a4bc5336a5f3920c7c8397de4d9cc8457 |
|
MD5 | 07f1768c4cfc011bc8442cbe7eb49577 |
|
BLAKE2b-256 | 387265300819f817f35165bab4194439d6c2f28b1f618f3f8d3fb7429ef24731 |