def print_acc2gi(accessions):
"""Print GIs corresponding to the given accession numbers."""
term = ' OR '.join(a + '[accn]' for a in accessions)
for line in entrez.on_search(db='nucleotide', term=term, tool='summary'):
if 'Name="Extra"' in line and any(a in line for a in accessions):
_, gi, _, acc, _ = line.split('|', 4)
print('%18s -> %s' % (acc, gi))
def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('-s', '--sra', metavar='SRAid', help='SRA identifier')
args = parser.parse_args()
for line in entrez.on_search(db='sra', term=args.sra, tool='summary'):
if 'Name="Runs"' in line:
acc = re.search('acc=\"(?P<acc>\w+[0-9]+)\"', line).group('acc')
print(acc)
def print_acc2gi(accessions):
"""Print GIs corresponding to the given accession numbers."""
term = ' OR '.join(a + '[accn]' for a in accessions)
for line in entrez.on_search(db='nucleotide', term=term, tool='summary'):
if 'Name="Extra"' in line and any(a in line for a in accessions):
gi = re.search('gi\|([0-9]+)\|', line).group(1)
acc = re.search('((emb)|(gb)|(ref)|(dbj))\|(?P<acc>\w+\.[0-9]+)\|',
line).group('acc')
print('%18s -> %s' % (acc, gi))
def print_acc2gi(accessions):
"""Print GIs corresponding to the given accession numbers."""
term = ' OR '.join(a + '[accn]' for a in accessions)
for line in entrez.on_search(db='nucleotide', term=term, tool='summary'):
if 'Name="Extra"' in line and any(a in line for a in accessions):
gi = re.search('gi\|([0-9]+)\|', line).group(1)
acc = re.search('((emb)|(gb)|(ref)|(dbj))\|(?P<acc>\w+\.[0-9]+)\|',
line).group('acc')
print('%18s -> %s' % (acc, gi))
def application_3():
"""Retrieving large datasets.
Download all chimpanzee mRNA sequences in FASTA format (>50,000 sequences).
"""
query = 'chimpanzee[orgn] AND biomol mrna[prop]'
with open('chimp.fna', 'w') as fout:
for line in entrez.on_search(db='nucleotide', term=query,
tool='fetch', rettype='fasta'):
fout.write(line + '\n')
def application_3():
"""Sample Application 3: Retrieving large datasets
Download all chimpanzee mRNA sequences in FASTA format (>50,000 sequences).
"""
query = 'chimpanzee[orgn] AND biomol mrna[prop]'
with open('chimp.fna', 'w') as fout:
for line in ez.on_search(db='nucleotide',
term=query,
tool='fetch',
rettype='fasta'):
fout.write(line + '\n')
print('The results are in file chimp.fna.')
def application_2():
"""Converting accession numbers to data.
Starting with a list of protein accession numbers, return the sequences in
FASTA format.
"""
# Input: comma-delimited list of accessions.
accs = 'NM_009417,NM_000547,NM_001003009,NM_019353'.split(',')
query = ' OR '.join(a + '[accn]' for a in accs)
# Output: FASTA data.
for line in entrez.on_search(db='nucleotide', term=query, tool='fetch',
db2='protein', rettype='fasta'):
print(line)
def application_2():
"""Sample Application 2: Converting accession numbers to data
Starting with a list of protein accession numbers, return the sequences in
FASTA format.
"""
# Input: comma-delimited list of accessions.
accs = 'NM_009417,NM_000547,NM_001003009,NM_019353'.split(',')
query = ' OR '.join(a + '[accn]' for a in accs)
# Output: FASTA data.
for line in ez.on_search(db='nuccore',
term=query,
tool='fetch',
rettype='fasta'):
print(line)
