Basics

🧬 Create a sequence

PyEED treats Protein sequences the same as DNA sequences. The central object of PyEED is the ProteinInfo and DNAInfo object, which both are an AbstractSequence.
A sequence object can be created by passing a sequence string to the constructor.

ProteinDNA

from pyeed.core import ProteinRecord

protein = ProteinRecord(
    name="My Protein",
    sequence="MTEITAAMVKELREDKAVQLLREKGLGK"
)

from pyeed.core import DNARecord

dna = DNARecord(sequence="ATGCGTACGTCGATCGATCGATCGATCGATCGATCGATCGATCGTAGTC")

🔎 Search for a sequence

Besides adding sequence information manually, PyEED also allows searching for sequences in the NCBI and UniProt databases. Therefore, the get_id() method can be used. In addition to the sequence itself, the method also returns the sequence's annotations and maps them to the corresponding attributes of the sequence object.

ProteinDNA

protein = ProteinRecord.get_id("UCS38941.1")

dna_record = DNARecord.get_id('AF188200.1')

⬇️ Save a sequence

To file

The sequence can be stored in a FASTA, JSON, YAML, or XML file format. Therefore, the respective method can be used. The methods below are written for protein, but can be used the same for dna_record The file path is passed as an argument to the method.

JSONYAMLXMLFASTA

protein.to_json("protein.json")

protein.to_yaml("protein.yaml")

protein.to_xml("protein.xml")

protein.to_fasta("protein.fasta")

To database

Alternatively, sequence data can be stored in a graph database. Therefore, the to_db() method can be used.

# Feature is currently implemented