Hi, I have trouble to down and save sequences from ncbi at one time. I get accession numbers using script:
from Bio import Entrez
def singleEntry(singleID): #the singleID is the accession number
handle = Entrez.efetch(db='nucleotide',id=singleID, rettype = 'fasta', retmode= 'text')
f = open('%s.fasta' % singleID, 'w')
f.write(handle.read())
handle.close()
f.close()
#get an id list: this makes a big search and gets a list of id
handle = Entrez.esearch(db='nucleotide', term = ["Poaceae[Orgn] AND als[Gene]"])
record = Entrez.read(handle)
handle.close()
print (record["IdList"])
I got IdList:
['1124779319', '1058275694', '160346987', '160346985', '313662298', '313662296', '313662294', '313662292', '148536620', '148536618', '944203885', '937553934', '698322664', '698322662', '698322660', '698322658', '683428019', '677285963', '677285961', '677285959']
Then, how to download those fasta sequences to one file? Thanks. I tried this:
from Bio import Entrez, SeqIO
def get_sequences(IdList):
ids = record["IdList"]
for seq_id in ids:
handle = Entrez.efetch(db="nucleotide", id="seq_id", rettype="fasta", retmode="text")
record = handle.read()
record = open('als.fasta', 'w')
record.write(record.rstrip('\n'))
but it showed: IndentationError: expected an indented block
•
written
by
HZZ0036 •
Your for loop needs to be indented.
This is not really a bioinformatics question but a Python programming question and as such it is better suited for https://stackoverflow.com/
record = open('als.fasta', 'w')
for seq_id in ids:
handle = Entrez.efetch(db="nucleotide", id="seq_id", rettype="fasta", retmode="text")
record = handle.read()
record.write(record.rstrip('\n'))
Ehm I also think OP and you are reusing/overwriting the variable name record.
I guess that's because you overwrite the record variable, you use it both for opening als.fasta and for reading the handle from efetch().
import os
from Bio import SeqIO
from Bio import Entrez
Entrez.email = "A.N.Other@example.com" # Always tell NCBI who you are
filename = "MG762674.fasta"
if not os.path.isfile(filename):
# Downloading...
net_handle = Entrez.efetch(
db="nucleotide", id="MG762674", rettype="fasta", retmode="text"
)
out_handle = open(filename, "w")
out_handle.write(net_handle.read())
out_handle.close()
net_handle.close()
print("Saved")
print("Parsing...")
record = SeqIO.read(filename, "fasta")
print(record)
Took this from Biopython Cookbook
You can pass a list for the of id. eg.
Accession_List = ['1124779319', '1058275694', '160346987', '160346985', '313662298', '313662296', '313662294', '313662292', '148536620', '148536618', '944203885', '937553934', '698322664', '698322662', '698322660', '698322658', '683428019', '677285963', '677285961', '677285959']
db="nucleotide", id=Accession_List, rettype="fasta", retmode="text"
This will save your file as one big fasta file Which you can split later, if you want, into files with individual sequences by using split fasta. i know i am answering late, but this is for anyone who washes up here having the same problem.
•
written
by
naman.misanthropist •
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hi, did you solve this?, i need to do the same