Good day,
Could you please help with my code: I need to convert from fasta file to json-object and I'm doing this via python dictionary. I have stock with two things:
from Bio import SeqIO
from Bio.SeqIO import parse
my_dict = {}
with open("Salm_ser_Enteritidis.fasta", 'r') as new_fasta:
for x in SeqIO.parse(new_fasta, 'fasta'):
dataset = x.id
sequence = x.seq
my_dict = {"dataset": x.id,
"sequence": x.seq}
print(my_dict)
Output is
{'dataset': 'PYJS01003085.1', 'sequence':
Seq('TCTCATCCGCCAAAACATCTTCGGCGTTGTAAGGTTAAGCCTCACGGTTCATTA...TTA')
but I need only actial sequence without word Seq for key 'sequence', so that output was:
{'dataset': 'PYJS01003085.1', 'sequence':
'TCTCATCCGCCAAAACATCTTCGGCGTTGTAAGGTTAAGCCTCACGGTTCATTA...TTA'
and the second problem:
import json
my_json = json.dumps(my_dict)
output TypeError: Object of type Seq is not JSON serializable
but via print(type(my_dict)) I have output that my_dict is <class 'dict'>, not type Seq. How to convert to dict for further # json?
Thanks in advance, Galina
•
written
by
biology.may20 •
Hi, you generate a SeqRecord Object and the seqrecord.seq is a seq object, not a string. You can convert it to a string with an explicit string cast (conversion) via str(seqrecord.seq), see here
from Bio import SeqIO
import json
# from Bio.SeqIO import parse # you won't need that, you imported the whole SeqIO package above
my_dict = {}
with open("Salm_ser_Enteritidis.fasta", 'r') as new_fasta:
for x in SeqIO.parse(new_fasta, 'fasta'):
# dataset = x.id
# sequence = x.seq # you won't need that, if the variables go out of scope and aren't used
my_dict = {
"dataset": x.id,
"sequence": str(x.seq) # string cast to SeqRecord seq object
}
my_json = json.dumps(my_dict) # maybe use json.dump directly to a file (use pretty print option, eg. indent=2)?
thank you a lot :)
I've used dump and now it's looks awsome !))
with open('my_dict.json', 'w') as f: json.dump(my_dict, f, indent=2)
Log in to answer this question.
please see: https://stackoverflow.com/questions/7100125/storing-python-dictionaries