Agent skill

bio-seq-objects

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SKILL.md

name: bio-seq-objects description: Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records. tool_type: python primary_tool: Bio.Seq measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:

  • read_file
  • run_shell_command

Seq Objects

Create and manipulate biological sequence objects using Biopython.

Required Imports

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

Core Objects

Seq - Immutable Sequence

The basic sequence object. Immutable like Python strings.

python
seq = Seq('ATGCGATCGATCG')

Seq objects support string-like operations:

python
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.

python
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

Convert between types:

python
seq = Seq(mut_seq)            # MutableSeq to Seq
mut_seq = MutableSeq(seq)     # Seq to MutableSeq

SeqRecord - Annotated Sequence

Sequence with metadata for file I/O and analysis.

python
record = SeqRecord(
    Seq('ATGCGATCG'),
    id='gene1',
    name='example_gene',
    description='An example gene sequence'
)

SeqRecord attributes:

python
record.seq           # The Seq object
record.id            # Identifier string
record.name          # Name string
record.description   # Description string
record.features      # List of SeqFeature objects
record.annotations   # Dict of annotations
record.letter_annotations  # Per-letter annotations (quality scores)
record.dbxrefs       # Database cross-references

SeqRecord Methods

Transform entire records while preserving metadata:

python
# Reverse complement (preserves ID, updates features)
rc_record = record.reverse_complement(id='gene1_rc', description='reverse complement')

# Translate to protein (creates new SeqRecord with protein)
protein_record = record.translate(id='gene1_protein')

# Quick format output (returns string in file format)
fasta_str = record.format('fasta')
genbank_str = record.format('genbank')

Slicing preserves features (adjusted to new coordinates):

python
# Slice SeqRecord - features are clipped/adjusted automatically
subset = record[10:50]  # Features outside range are dropped

Code Patterns

Create Seq from String

python
dna = Seq('ATGCGATCGATCG')
rna = Seq('AUGCGAUCGAUCG')
protein = Seq('MRCRS')

Create SeqRecord for File Output

python
record = SeqRecord(Seq('ATGCGATCG'), id='seq1', description='My sequence')

Create SeqRecord with Annotations

python
record = SeqRecord(Seq('ATGCGATCG'), id='gene1', description='Example')
record.annotations['organism'] = 'Homo sapiens'
record.annotations['molecule_type'] = 'DNA'

Build SeqRecord from Parsed Data

python
from Bio.SeqFeature import SeqFeature, FeatureLocation

record = SeqRecord(Seq('ATGCGATCGATCG'), id='gene1')
feature = SeqFeature(FeatureLocation(0, 9), type='CDS', qualifiers={'product': ['Example protein']})
record.features.append(feature)

Batch Create SeqRecords

python
sequences = ['ATGC', 'GCTA', 'TTAA']
records = [SeqRecord(Seq(s), id=f'seq_{i}') for i, s in enumerate(sequences)]

Copy a SeqRecord

python
from copy import deepcopy
new_record = deepcopy(record)
new_record.id = 'modified_copy'

Modify SeqRecord Sequence

python
record = SeqRecord(Seq('ATGCGATCG'), id='seq1')
record.seq = Seq('GGGGGATCG')  # Replace entire sequence

Join Sequences into One SeqRecord

python
combined_seq = seq1 + Seq('NNNN') + seq2  # With linker
combined_record = SeqRecord(combined_seq, id='combined')

Transform SeqRecord with reverse_complement

python
# Reverse complement a gene sequence
record = SeqRecord(Seq('ATGCGATCGATCG'), id='gene1', description='Forward strand')
rc_record = record.reverse_complement(id=f'{record.id}_rc', description='Reverse complement')
# Features are remapped to new coordinates

Translate SeqRecord to Protein

python
# Translate coding sequence
cds_record = SeqRecord(Seq('ATGCGATCGATCGTAA'), id='cds1', description='Coding sequence')
protein_record = cds_record.translate(id=f'{cds_record.id}_protein', to_stop=True)

Quick Output with format()

python
record = SeqRecord(Seq('ATGCGATCG'), id='seq1', description='Example sequence')
print(record.format('fasta'))
# >seq1 Example sequence
# ATGCGATCG

Common Errors

Error Cause Solution
TypeError: 'Seq' object does not support item assignment Trying to modify immutable Seq Use MutableSeq instead
TypeError: SeqRecord object argument must be a Seq object Passed string instead of Seq Wrap string in Seq()
Missing annotations in output Didn't set required annotations Add molecule_type to annotations for GenBank output

Decision Tree

Need to work with sequence data?
├── Just doing string-like operations?
│   └── Use Seq
├── Need to modify sequence in-place?
│   └── Use MutableSeq
├── Need metadata (ID, description, features)?
│   └── Use SeqRecord
└── Need to write to file?
    └── Use SeqRecord with appropriate annotations

Related Skills

  • sequence-io/read-sequences - Parse files to get SeqRecord objects
  • sequence-io/write-sequences - Write SeqRecord objects to files
  • transcription-translation - Transform Seq objects (DNA to protein)
  • reverse-complement - Get reverse complement of Seq
  • sequence-slicing - Slice and extract from Seq/SeqRecord
  • database-access/entrez-fetch - Fetch sequences from NCBI as SeqRecords

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