Loading debian/tests/fetch_test_data.py 0 → 100755 +44 −0 Original line number Diff line number Diff line #!/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/gingo.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('rbcL-primer.txt', 'w') pf.write(pr) pf.write('\n') pf.close() fetch_ids(database, query) create_primer(primer) Loading
debian/tests/fetch_test_data.py 0 → 100755 +44 −0 Original line number Diff line number Diff line #!/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/gingo.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('rbcL-primer.txt', 'w') pf.write(pr) pf.write('\n') pf.close() fetch_ids(database, query) create_primer(primer)