Create restriction maps showing enzyme cut positions on DNA sequences using Biopython Bio.Restriction. Visualize cut sites, calculate distances between sites, and generate text or graphical maps. Use when creating or analyzing restriction maps.
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')
# 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')
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')
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}')
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)
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})')
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)
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}')