Biopython -- SeqRecord

手动创建SeqRecord

from Bio.SeqRecord import SeqRecord
#help(SeqRecord)

#creat a SeqRecord
from Bio.Seq import Seq
simple_seq = Seq("GATCGATC")
simple_seq_r  = SeqRecord(simple_seq) #可以同时指定id，description，name等属性，也可以随后重新赋值

simple_seq_r.id

'<unknown id>'

simple_seq_r.id = "ACT001.1"
simple_seq_r.id

'ACT001.1'

simple_seq_r.description

'<unknown description>'

simple_seq_r.description = "this is a test!"
simple_seq_r.description

'this is a test!'

simple_seq_r.seq

Seq('GATCGATC', Alphabet())

#SeqRecord 有一个annotation属性，会以字典的形式记录注释信息
simple_seq_r.annotations["evidence"] = "None. I just make it up"
print(simple_seq_r.annotations)
print("===========")
print(simple_seq_r.annotations["evidence"])

{'evidence': 'None. I just make it up'}
===========
None. I just make it up

SeqRecord object from Fasta files

#SeqRecord object from Fasta files
from Bio import SeqIO
record = SeqIO.read("NC_005816.fna","fasta")
record.id

SeqRecord object from GenBank files

#SeqRecord object from GenBank files
record = SeqIO.read("NC_005816.gb","genbank")
record
record.seq