Biopython

Biopython is the long-standing, general-purpose toolkit for biological computation in Python. If you have ever parsed a FASTA file in Python, you have probably used it.

Highlights

• Read/write dozens of formats (FASTA, FASTQ, GenBank, PDB, Clustal…).
• Sequence objects, alignments, BLAST parsing and Entrez/NCBI access.
• 3D structure parsing via Bio.PDB.

Example

1from Bio import SeqIO
2for rec in SeqIO.parse("seqs.fasta", "fasta"):
3    print(rec.id, len(rec.seq), rec.seq.translate())
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