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CDS_extractor.py
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CDS_extractor.py
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import numpy as np
import os
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
counter = 0
CDS_records = []
database_path = os.path.join(os.getcwd(), 'Data_2', 'database.gb')
write_path = os.path.join(os.getcwd(), 'Data_3', 'MCP_database.fasta')
for record in SeqIO.parse(database_path, 'gb'):
for feature in record.features:
if feature.type == 'CDS':
for qualifiers in feature.qualifiers:
if qualifiers == 'product':
for product in feature.qualifiers['product']:
if feature.qualifiers['product'] == ['Major capsid protein']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['major capsid protein']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['UL19']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['40']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['UL86']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['U57']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['BcLF1']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
elif feature.qualifiers['product'] == ['ORF25']:
CDS = feature.location.extract(record)
sequence = SeqRecord(CDS.seq, id=record.id,
description=record.description)
counter += 1
CDS_records.append(sequence)
SeqIO.write(CDS_records, write_path, 'fasta')
print(counter)