1. Essential BioPython Retrieving Sequences from the Web
MARC: Developing Bioinformatics Programs
Alex Ropelewski
PSC-NRBSC
Bienvenido Vélez
UPR Mayaguez

2. The Entrez eFetch Function
Fetching a single Genbank Sequence from the Network
from Bio import SeqIO
from Bio import Entrez
#Please use your REAL address below:
handle = Entrez.efetch(db="nucleotide",rettype="gb",id="NM_000518")
sr = SeqIO.read(handle,"genbank")
print sr.id
print sr.seq
handle.close()

3. Main eFetch Function Parameters
Name
Req’d
Default
Description with Options db Y
N/A
Database to search** (e.g. nucleotide, protein, structure) id
Single of comma separated list of unique IDs**
retmode N
db specific
Data format for records returned* (text, xml or asn.1.)
rettype
Data layout for records returned* (e.g. fasta, gp)
retstart
Sequential index of first record to be retrieved
Retmax
10,000
Max number of records to retrieve
seq_start 1
First sequence base to retrieve
seq_stop
length
Last sequence base to retrieve
*See for a complete list of available retmode/rettype combinations
**See for a complete list of avalable Entrez databases and their corresponding unique identifiers.

4. The Entrez eFetch Function
Fetch a single Genbank Sequence from the Network and Save
from Bio import SeqIO
from Bio import Entrez
InHandle = Entrez.efetch(db="nucleotide",rettype="gb",id="NM_000518")
sr = SeqIO.read(InHandle, "genbank")
OutHandle = open("NM_ gb","w")
SeqIO.write(sr,OutHandle,"genbank")
InHandle.close()
OutHandle.close()

5. The Entrez eFetch Function
Fetch a single Genbank Sequence from the Network and Save as Fasta
from Bio import SeqIO
from Bio import Entrez
InHandle = Entrez.efetch(db="nucleotide",rettype="gb",id="NM_000518")
sr = SeqIO.read(InHandle, "genbank")
OutHandle = open("NM_ fasta","w")
SeqIO.write(sr,OutHandle,"fasta")
InHandle.close()
OutHandle.close()

6. The Entrez eFetch Function
Fetch multiple Genbank Sequences from the Network and Save as Fasta
from Bio import SeqIO
from Bio import Entrez
accessions="NM_000518, AJ131351"
InHandle = Entrez.efetch(db="nucleotide",rettype="gb",id=accessions)
seqRecords = SeqIO.parse(InHandle, "genbank")
OutHandle = open("myseqs.fasta","w")
SeqIO.write(seqRecords,OutHandle,"fasta")
InHandle.close()
OutHandle.close()

7. The ExPASy and SwissProt Packages
Fetch SwissProt Sequences from ExPASy and Save as Fasta
>>> from Bio import ExPASy
>>> from Bio import SeqIO
>>> accessions = ["O23729", "O23730", "O23731"]
>>> records = []
>>> for accession in accessions:
... handle = ExPASy.get_sprot_raw(accession)
... record = SeqIO.read(handle, "swiss")
... records.append(record)
>>> outHandle=open("mysequences.fasta", "w")
>>> SeqIO.write(records,outHandle,"fasta")
>>> outHandle.close()