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: ◊◊◊◊◊◊◊◊◊◊◊◊◊◊◊
1 maintainer
Metadata
1 maintainer
Release files for pyoinformatics 0.2.5
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
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| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pyoinformatics-0.2.5-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 13.3 kB
Release files / pyoinformatics-0.2.5.tar.gz
| Download URL | pyoinformatics-0.2.5.tar.gz |
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Release files / pyoinformatics-0.2.5-py3-none-any.whl
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