A simple bioinformatics package
Project description
pyoinformatics ๐
pip install pyoinformatics
Examples
Find the reverse complement of all the sequences in a file:
with open('out.fasta', 'w') as f:
for seq in Bio.read_fasta('in.fasta'):
f.writelines(seq.reverse_complement().to_fasta())
Count the number of occurrences of 'ATG' in seq1
seq1.count('ATG')
Count the number of occurrences of 'ATG' in seq1 that differ by <= 1 base.
seq1.count('ATG', 1)
Find the number of occurrences of 'ATG' or 'AAG' in seq1
len(seq1.find('A[AT]G'))
Find the average position of all occurrences of 'ATG' in a fasta file
from statistics import mean
for seq in Bio.read_fasta('in.fasta'):
print(mean(seq.find('ATG')))
ASCI plot the relative nt counts for all the sequences in a file
for seq in Bio.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
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