def __init__(self, s=None, ps=None):
if isinstance(s, basestring):
self.sequence = Seq(s)
else:
self.sequence = s
self.prosite = ExPASy.get_prosite_raw(ps)
self.record = Prosite.read(self.prosite)
self.pat = pa.compile(self.record.pattern)
self.regexp = re.compile(pa.prosite_to_re(self.record.pattern))
tests = [ 'ps00107.txt',
'ps00159.txt',
'ps00165.txt',
'ps00432.txt',
'ps00488.txt',
'ps00546.txt' ]
def print_list( list ):
for item in list:
print( ' ' + str( item ) )
for test in tests:
print "testing %s" % test
datafile = os.path.join( 'Prosite', test )
src_handle = open(datafile)
data = Prosite.read(src_handle)
print data.name
print data.type
print data.accession
print data.created
print data.data_update
print data.info_update
# print data.data_info
print data.pdoc
print data.description
print data.pattern
print data.matrix
print data.rules
print data.nr_sp_release
print data.nr_sp_seqs
print data.cc_taxo_range
import os
from Bio import Prosite
tests = ["ps00107.txt", "ps00159.txt", "ps00165.txt", "ps00432.txt", "ps00488.txt", "ps00546.txt"]
def print_list(list):
for item in list:
print (" " + str(item))
for test in tests:
print "testing %s" % test
datafile = os.path.join("Prosite", test)
src_handle = open(datafile)
data = Prosite.read(src_handle)
print data.name
print data.type
print data.accession
print data.created
print data.data_update
print data.info_update
# print data.data_info
print data.pdoc
print data.description
print data.pattern
print data.matrix
print data.rules
print data.nr_sp_release
print data.nr_sp_seqs
print data.cc_taxo_range