biology-biopython
Installation
SKILL.md
Biopython Bioinformatics Best Practice
Sequence Manipulation
- Create sequences:
from Bio.Seq import Seq; seq = Seq("ATGCGA") - Complement:
seq.complement(); Reverse complement:seq.reverse_complement() - Transcription:
seq.transcribe()(DNA to RNA) - Translation:
seq.translate()(DNA/RNA to protein) - GC content:
from Bio.SeqUtils import gc_fraction; gc_fraction(seq) - Molecular weight:
from Bio.SeqUtils import molecular_weight
File Parsing (SeqIO)
- Read FASTA:
for rec in SeqIO.parse("file.fasta", "fasta"): ... - Read GenBank:
for rec in SeqIO.parse("file.gb", "genbank"): ... - Read single record:
rec = SeqIO.read("file.fasta", "fasta") - Write sequences:
SeqIO.write(records, "output.fasta", "fasta") - Convert formats:
SeqIO.convert("input.gb", "genbank", "output.fasta", "fasta") - Index large files:
idx = SeqIO.index("large.fasta", "fasta")for random access