1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
|
#!/usr/bin/python3
# Fetching the required data for testing
# a. entrez NCBI fasta test file
# b. a primer data file
from Bio import Entrez
Entrez.email = 'unknown@debian.org'
database = 'nucleotide'
fn = 'data/gingko.fasta'
query = [
'((chloroplast OR plastid) AND "complete genome" AND Embryophyta NOT (mi- tochondrion OR mitochondrial)) AND "Ginkgo biloba"'
]
primer = "rbcL1/rbcLA\t TTGGCAGCATTYCGAGTAACTCC\t CCTTTRTAACGATCAAGRC"
def fetch_ids(dbs, qr):
# Fetch the query IDs
print(dbs, qr)
handle = Entrez.esearch(db=dbs, term=qr)
record = Entrez.read(handle)
ids = record['IdList']
handle.close()
# Fetch the first result
ff = open(fn, 'w')
handle_fasta = Entrez.efetch(
db=dbs, id=ids[0], rettype='fasta', retmode='text')
ff.write(handle_fasta.read().rstrip('\n'))
handle_fasta.close()
def create_primer(pr):
pf = open('data/rbcL-primer.txt', 'w')
pf.write(pr)
pf.write('\n')
pf.close()
fetch_ids(database, query)
create_primer(primer)
|
