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What is the equivalent function in Biopython for BioPerl's Bio::DB::Fasta?

I'm translating a Perl code to a Python code using BioPython.

I got something like:

my $db = Bio::DB::Fasta->new($path,$options)

and I'm looking for a similar function in Biopython. Is there anything like this?

Solution

  • You can find the IO for FASTA files at http://biopython.org/DIST/docs/api/Bio.SeqIO-module.html

    About the indexing, I think Biopython doesn't handle '.fai' files like Bio::DB:Fasta. You can have a dictionary (like a perl hash) using the SeqIO.index() method. This is a quick example as shown in the docs:

    from Bio import SeqIO
record_dict = SeqIO.index("fasta_file.fas", "fasta")

print(record_dict["ID of the fasta sequence"])

    SeqIO.index creates a dict in memory to allow random access to each sequence. Read the docs to view the limitations of that dict: http://biopython.org/DIST/docs/api/Bio.File._IndexedSeqFileDict-class.html