I have to download only complete genome sequences from NCBI (GenBank(full) format). I am intrested in ‘complete geneome’ not ‘whole genome’.,Here is my code for Complete Genome Sequence Parsing into .FASTA files…,You will see there are only six complete E.Coli reference genomes in NCBI (www.ncbi.nlm.nih.gov/genome/167):,To help you, here are the Genbank/Refseq links to their genomes:
Here is my code for Complete Genome Sequence Parsing into .FASTA files…
# Imports
from Bio
import Entrez
from Bio
import SeqIO
# # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Retrieve NCBI Data Online #
# # # # # # # # # # # # # # # # # # # # # # # # # # # # #
Entrez.email = "asiak@wp.pl"
# Always tell NCBI who you are
genomeAccessions = ['NC_000913', 'NC_002695', 'NC_011750', 'NC_011751', 'NC_017634', 'NC_018658']
search = " ".join(genomeAccessions)
handle = Entrez.read(Entrez.esearch(db = "nucleotide", term = search, retmode = "xml"))
genomeIds = handle['IdList']
records = Entrez.efetch(db = "nucleotide", id = genomeIds, rettype = "gb", retmode = "text")
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Generate Genome Fasta files #
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
sequences = [] # store your sequences in a list
headers = [] # store genome names in a list(db_xref ids)
for i, record in enumerate(records):
file_out = open("genBankRecord_" + str(i) + ".gb", "w") # store each genomes.gb in separate files
file_out.write(record.read())
file_out.close()
genomeGenbank = SeqIO.read("genBankRecord" + str(i) + ".gb", "genbank") # parse in the genbank files
header = genome.features[0].qualifiers['db_xref'][0] # name the genome using db_xfred ID
sequence = genome.seq.tostring() # obtain genome sequence
headers.append('>' + header) # store genome name in list
sequences.append(sequence) # store sequence in list
fasta_out = open("genome" + str(i) + ".fasta", "w") # store each genomes.fasta in separate files
fasta_out.write(header) # > header...followed by:
fasta_out.write(sequence) # sequence...
fasta_out.close() # close that.fasta file and move on to next genome
records.close()
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esearch Searches and retrieves primary IDs (for use in EFetch, ELink,
and ESummary) and term translations and optionally retains
results for future use in the user’s environment.,ESearch searches and retrieves primary IDs (for use in EFetch, ELink
and ESummary) and term translations, and optionally retains results
for future use in the user’s environment.,This will automatically use an HTTP POST rather than HTTP GET if there
are over 200 identifiers as recommended by the NCBI.,Parse an XML file from the NCBI Entrez Utilities into python objects.
>>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> handle = Entrez.einfo() # or esearch, efetch, ... >>> record = Entrez.read(handle) >>> handle.close()
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Hi, I have trouble to down and save sequences from ncbi at one time. I get accession numbers using script:,Then, how to download those fasta sequences to one file? Thanks. I tried this:,This is not really a bioinformatics question but a Python programming question and as such it is better suited for stackoverflow.com/,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().
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"])
['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'))
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One common usage is downloading sequences in the FASTA or
GenBank/GenPept plain text formats (which can then be parsed with
Bio.SeqIO, see Sections 5.3.1
and 9.6). From the Cypripedioideae example above,
we can download GenBank record 186972394 using Bio.Entrez.efetch:,One obvious case is you may prefer to download sequences in the FASTA or
GenBank/GenPept plain text formats (which can then be parsed with
Bio.SeqIO, see Sections 5.3.1
and 9.6). For the literature databases, Biopython
contains a parser for the MEDLINE format used in PubMed.,The arguments rettype=”gb” and retmode=”text” let us download
this record in the GenBank format.,Now we download the list of GenBank identifiers:
>>> from Bio
import Entrez
>>>
Entrez.email = "A.N.Other@example.com"
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Genome (Whole Genome Database),Protein (Sequence Database),Nucleotide (GenBank Sequence Database),Structure (Three Dimensional Macromolecular Structure)
To add the features of Entrez, import the following module −
>>> from Bio
import Entrez
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You will use the extract_insdc() function to get the accession IDs for the sequences in this Ralstonia solanacearum genome, in the cell below.,By running the cell below, you can see that each sequence in the Ralstonia solanacearum assembly has been downloaded into a SeqRecord, and that it contains useful metadata, describing the sequence assembly and properties of the annotation.,In this section, you will use one of the database identifiers returned from your search at NCBI to identify and download the GenBank records corresponding to a single assembly of Ralstonia solanacearum.,Now we have accession UIDs for the nucleotide sequences of the assembly, you will use Entrez.efetch as before to fetch each sequence record from NCBI.
If this is successful, you should see the input marker to the left of the cell change from
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