scbirlab / streq

🧬 Python utilities for working with nucleotide sequence strings.

🧬 streq

Python utilities for working with nucleotide sequence strings.

Installation

The easy way

Install the pre-compiled version from PyPI:

pip install streq

From source

Clone the repository, then cd into it. Then run:

pip install -e .

Usage

Streq provides various utility functions in Python for working with nucleotide sequences. Sequences can be upper or lower case, and case will be preserved through transformations.

Transformations

Reverse complement.

>>> import streq as sq
>>>
>>> sq.reverse_complement('ATCG')
'CGAT'

Convert between RNA and DNA alphabets.

>>> sq.to_rna('ATCG')
'AUCG'
>>> sq.to_dna('AUCG')
'ATCG'

Slice circular sequences such as plasmids or bacterial genomes.

>>> sq.Circular('ATCG')[-1:3]
'GATC'
>>> sq.reverse_complement(sq.Circular('ATCG'))[-1:3]
'CGAT'

Cases are preserved throughout the transformations.

>>> sq.reverse_complement(sq.Circular('ATCg'))
'cGAT'

Calculations

Get GC and pyrimidine content.

>>> sq.gc_content('AGGG')
0.75
>>> sq.pyrimidine_content('AUGGG')
0.2

Get autocorrelation (rough indicator for secondary structure).

>>> sq.correlation('AACC')
0.0
>>> sq.correlation('AAATTT')
2.3
>>> sq.correlation('AAATTCT')
1.3047619047619046
>>> sq.correlation('AAACTTT')
1.9238095238095236

Wobble base-pairing can be taken into account.

>>> correlation('GGGTTT')
0.0
>>> correlation('GGGTTT', wobble=True)
2.3
>>> correlation('GGGUUU', wobble=True)
2.3

Provide a second sequence to get correlation between sequences.

>>> sq.correlation('AAA', 'TTT')
0.0
>>> sq.correlation('AAA', 'AAA')
3.0

Distances

Calculate Levenshtein (insert, delete, mutate) distance.

>>> sq.levenshtein('AAATTT', 'AAATTT')
0
>>> sq.levenshtein('AAATTT', 'ACTTT')
2
>>> sq.levenshtein('AAAG', 'TCGA')
4

Calculate Hamming (mismatch) distance.

>>> sq.hamming('AAA', 'ATA')
1
>>> sq.hamming('AAA', 'ATT')
2
>>> sq.hamming('AAA', 'TTT')
3

Search

Search sequences using IUPAC symbols and iterate through the results.

>>> for (start, end), match in sq.find_iupac('ARY', 'AATAGCAGTGTGAAC'):
...     print(f"Found ARY at {start}:{end}: {match}")
... 
Found ARY at 0:3: AAT
Found ARY at 3:6: AGC
Found ARY at 6:9: AGT
Found ARY at 12:15: AAC

Find common Type IIS restriction sites:

>>> sq.which_re_sites('AAAGAAG')
()
>>> sq.which_re_sites('AAAGAAGAC')
('BbsI',)
>>> sq.which_re_sites('AAAGAAGACACCTGC')
('BbsI', 'PaqCI')

Documentation

Check the API here.

streq's Issues

Add amino acids to sequences

Currently utils.sequences only provides nucleotides. It would be helpful to have an amino acid alphabet too.