def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a Prodoc entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
import time
from Bio.WWW import ExPASy
# First, check to see if enough time has passed since my
# last query.
if self.last_query_time is not None:
delay = self.last_query_time + self.delay - time.time()
if delay > 0.0:
time.sleep(delay)
self.last_query_time = time.time()
try:
handle = ExPASy.get_prodoc_entry(id)
except IOError:
raise KeyError, id
try:
handle = File.StringHandle(_extract_record(handle))
except ValueError:
raise KeyError, id
if self.parser is not None:
return self.parser.parse(handle)
return handle.read()
def scan_sequence_expasy(seq=None, id=None, exclude_frequent=None):
"""scan_sequence_expasy(seq=None, id=None, exclude_frequent=None) ->
list of PatternHit's
Search a sequence for occurrences of Prosite patterns. You can
specify either a sequence in seq or a SwissProt/trEMBL ID or accession
in id. Only one of those should be given. If exclude_frequent
is true, then the patterns with the high probability of occurring
will be excluded.
"""
from Bio import ExPASy
if (seq and id) or not (seq or id):
raise ValueError, "Please specify either a sequence or an id"
handle = ExPASy.scanprosite1(seq, id, exclude_frequent)
return _extract_pattern_hits(handle)
def sprot_search(accs, outf=sys.stdout):
all_results = ''
i=0
for acc in accs:
outf.write('>'+acc+'\n')
sys.stderr.write( acc + "\tNo. " + repr(i) +'\n')
try:
results=ExPASy.get_sprot_raw(acc)
outf.write(results.read())
except IOError:
sys.stderr.write( "I/O error: No results \n")
i=i+1
def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a SwissProt entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
# First, check to see if enough time has passed since my
# last query.
self.limiter.wait()
try:
handle = ExPASy.get_sprot_raw(id)
except IOError:
raise KeyError, id
if self.parser is not None:
return self.parser.parse(handle)
return handle.read()
def __getitem__(self, id):
"""__getitem__(self, id) -> object
Return a Prosite entry. id is either the id or accession
for the entry. Raises a KeyError if there's an error.
"""
from Bio.WWW import ExPASy
# First, check to see if enough time has passed since my
# last query.
self.limiter.wait()
try:
handle = ExPASy.get_prosite_entry(id)
except IOError:
raise KeyError, id
try:
handle = File.StringHandle(_extract_record(handle))
except ValueError:
raise KeyError, id
if self.parser is not None:
return self.parser.parse(handle)
return handle.read()
"""Example of connecting with exPASy and parsing SwissProt records."""
# standard library
import string
# biopython
from Bio.WWW import ExPASy
from Bio.SwissProt import SProt
from Bio import File
# 'O23729', 'O23730', 'O23731', Chalcone synthases from Orchid
ids = ['O23729', 'O23730', 'O23731']
all_results = ''
for id in ids:
results = ExPASy.get_sprot_raw(id)
all_results = all_results + results.read()
s_parser = SProt.RecordParser()
s_iterator = SProt.Iterator(File.StringHandle(all_results), s_parser)
while 1:
cur_record = s_iterator.next()
if cur_record is None:
break
print "description:", cur_record.description
for ref in cur_record.references:
print "authors:", ref.authors
print "title:", ref.title
