bio-restriction-mapping

What this skill does

## 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.

# Restriction Mapping

**"Create a restriction map of my sequence"** -> Visualize cut site positions for multiple enzymes along a DNA sequence with inter-site distances.
- Python: `Bio.Restriction.Analysis` for positions, `matplotlib` for graphical maps

## Create Basic Restriction Map

```python
from Bio import SeqIO
from Bio.Restriction import EcoRI, BamHI, HindIII, RestrictionBatch, Analysis

record = SeqIO.read('sequence.fasta', 'fasta')
seq = record.seq

batch = RestrictionBatch([EcoRI, BamHI, HindIII])
analysis = Analysis(batch, seq)

# Print formatted map
analysis.print_as('map')
```

## Output Formats

```python
# Map format (visual)
analysis.print_as('map')

# Linear format (list)
analysis.print_as('linear')

# Tabular format
analysis.print_as('tabulate')

# Get as string instead of printing
map_str = analysis.format_as('map')
linear_str = analysis.format_as('linear')
```

## Calculate Distances Between Sites

```python
from Bio.Restriction import EcoRI, BamHI

ecori_sites = EcoRI.search(seq)
bamhi_sites = BamHI.search(seq)

# All cut positions sorted
all_sites = sorted(ecori_sites + bamhi_sites)

# Calculate distances between consecutive sites
distances = []
for i in range(len(all_sites) - 1):
    dist = all_sites[i + 1] - all_sites[i]
    distances.append((all_sites[i], all_sites[i + 1], dist))
    print(f'{all_sites[i]} -> {all_sites[i + 1]}: {dist} bp')
```

## Create Detailed Restriction Map

```python
from Bio import SeqIO
from Bio.Restriction import RestrictionBatch, Analysis
from Bio.Restriction import EcoRI, BamHI, HindIII, XhoI, NotI

record = SeqIO.read('plasmid.fasta', 'fasta')
seq = record.seq
seq_len = len(seq)

enzymes = RestrictionBatch([EcoRI, BamHI, HindIII, XhoI, NotI])
analysis = Analysis(enzymes, seq, linear=False)

print(f'Restriction Map: {record.id}')
print(f'Length: {seq_len} bp (circular)')
print('=' * 50)

results = analysis.full()
all_cuts = []

for enzyme, sites in results.items():
    for site in sites:
        all_cuts.append((site, str(enzyme)))

all_cuts.sort(key=lambda x: x[0])

print('\nCut sites (5\' -> 3\'):')
for pos, enz in all_cuts:
    pct = (pos / seq_len) * 100
    print(f'  {pos:6d} bp ({pct:5.1f}%) - {enz}')
```

## Text-Based Map Visualization

```python
def draw_restriction_map(seq, results, width=80):
    '''Draw a simple text restriction map'''
    seq_len = len(seq)
    scale = width / seq_len

    # Header
    print(f'0{" " * (width - 6)}{seq_len}')
    print('|' + '-' * (width - 2) + '|')

    # Plot each enzyme
    for enzyme, sites in results.items():
        if not sites:
            continue
        line = [' '] * width
        for site in sites:
            pos = int(site * scale)
            if pos >= width:
                pos = width - 1
            line[pos] = '|'
        print(''.join(line) + f' {enzyme}')

    print('|' + '-' * (width - 2) + '|')

# Usage
batch = RestrictionBatch([EcoRI, BamHI, HindIII])
analysis = Analysis(batch, seq)
results = analysis.full()
draw_restriction_map(seq, results)
```

## Map with GenBank Features

```python
from Bio import SeqIO
from Bio.Restriction import RestrictionBatch, Analysis, EcoRI, BamHI

record = SeqIO.read('plasmid.gb', 'genbank')
seq = record.seq

enzymes = RestrictionBatch([EcoRI, BamHI])
analysis = Analysis(enzymes, seq, linear=False)
results = analysis.full()

print('Restriction Sites and Overlapping Features:')
print('=' * 60)

for enzyme, sites in results.items():
    for site in sites:
        print(f'\n{enzyme} at position {site}:')
        for feature in record.features:
            start = int(feature.location.start)
            end = int(feature.location.end)
            if start <= site <= end:
                feat_type = feature.type
                label = feature.qualifiers.get('label', feature.qualifiers.get('gene', ['unknown']))[0]
                print(f'  Within {feat_type}: {label} ({start}-{end})')
```

## Export Map to File

```python
def export_restriction_map(seq, results, output_file, seq_name='sequence'):
    '''Export restriction map to text file'''
    with open(output_file, 'w') as f:
        f.write(f'Restriction Map: {seq_name}\n')
        f.write(f'Length: {len(seq)} bp\n')
        f.write('=' * 50 + '\n\n')

        all_cuts = []
        for enzyme, sites in results.items():
            for site in sites:
                all_cuts.append((site, str(enzyme)))

        all_cuts.sort()

        f.write('Site\tPosition\tFrom_Start\n')
        for pos, enz in all_cuts:
            f.write(f'{enz}\t{pos}\t{pos}\n')

        f.write('\n\nFragment sizes between sites:\n')
        if all_cuts:
            positions = sorted([c[0] for c in all_cuts])
            for i in range(len(positions) - 1):
                size = positions[i + 1] - positions[i]
                f.write(f'{positions[i]} -> {positions[i + 1]}: {size} bp\n')

# Usage
export_restriction_map(seq, results, 'restriction_map.txt', record.id)
```

## Circular Map Coordinates

```python
def circular_distances(sites, seq_len):
    '''Calculate fragment sizes for circular DNA'''
    if not sites:
        return []

    sites = sorted(sites)
    fragments = []

    # Between consecutive sites
    for i in range(len(sites) - 1):
        fragments.append(sites[i + 1] - sites[i])

    # Wrap-around fragment
    wrap = (seq_len - sites[-1]) + sites[0]
    fragments.append(wrap)

    return fragments

# Usage
ecori_sites = EcoRI.search(seq, linear=False)
fragments = circular_distances(ecori_sites, len(seq))
print(f'EcoRI fragments (circular): {fragments}')
```

## Related Skills

- restriction-sites - Find where enzymes cut
- enzyme-selection - Choose enzymes for mapping
- fragment-analysis - Analyze fragment sizes