bio-seq-objects

Version Compatibility

Reference examples tested with: BioPython 1.83+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Seq Objects

Create and manipulate biological sequence objects using Biopython.

"Create a sequence object" → Wrap a raw string in a typed sequence container for biological operations.

• Immutable: Seq('ATGC') (BioPython) — string-like, supports complement/translate
• Mutable: MutableSeq('ATGC') (BioPython) — supports in-place edits
• Annotated: SeqRecord(Seq(...), id=...) (BioPython) — adds metadata for file I/O

Required Imports

from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord

Core Objects

Seq - Immutable Sequence

The basic sequence object. Immutable like Python strings.

seq = Seq('ATGCGATCGATCG')

Seq objects support string-like operations:

len(seq)           # Length
seq[0]             # First base
seq[-1]            # Last base
seq[0:10]          # Slice (returns Seq)
str(seq)           # Convert to string
'ATG' in seq       # Membership test
seq.count('G')     # Count occurrences
seq.find('ATG')    # Find position (-1 if not found)
seq.upper()        # Uppercase
seq.lower()        # Lowercase
seq * 3            # Repeat sequence
seq.strip()        # Remove leading/trailing whitespace

MutableSeq - Mutable Sequence

For in-place modifications when performance matters.

mut_seq = MutableSeq('ATGCGATCG')
mut_seq[0] = 'C'              # Modify single position
mut_seq[0:3] = 'GGG'          # Replace slice
mut_seq.append('A')           # Add to end
mut_seq.insert(0, 'G')        # Insert at position
mut_seq.pop()                 # Remove and return last
mut_seq.remove('G')           # Remove first occurrence
mut_seq.reverse()             # Reverse in place