# Copyright 2001 by Iddo Friedberg. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. from Bio import FSSP from Bio.FSSP import FSSPTools import sys import os # import pickle test_file = os.path.join('FSSP', '1cnv.fssp') f = sys.stdout f.write("\nRead in %s\n" % os.path.basename(test_file)) handle = open(test_file) head_rec, sum_rec, align_rec = FSSP.read_fssp(handle) handle.close() f.write("...1cnv.fssp read\n") for i in [ "author", "compnd", "database", "header", "nalign", "pdbid", "seqlength", "source" ]: f.write('head_rec.%s %s\n' % (i, str(getattr(head_rec, i)))) f.write("\nlen(sum_rec) = %d; head_rec.nalign = %d\n" % (len(sum_rec), head_rec.nalign)) f.write("The above two numbers should be the same\n") f.write("\nCreate a multiple alignment instance using Bio.Align\n") alignment = FSSPTools.mult_align(sum_rec, align_rec) f.write("...Done\n") # Percent ID filtering takes too long.. remove from test.
def setUpClass(cls): path = os.path.join("FSSP", "1cnv.fssp") handle = open(path) cls.head_rec, cls.sum_rec, cls.align_rec = FSSP.read_fssp(handle) handle.close()
def setUpClass(cls): path = os.path.join("FSSP", "1cnv.fssp") with open(path) as handle: cls.head_rec, cls.sum_rec, cls.align_rec = FSSP.read_fssp(handle)
from Bio import FSSP, Align from Bio.FSSP import FSSPTools import sys import os import cPickle import time test_file = os.path.join('FSSP', '1cnv.fssp') f = sys.stdout f.write("\nRead in %s\n" % os.path.basename(test_file)) handle = open(test_file) head_rec, sum_rec, align_rec = FSSP.read_fssp(handle) handle.close() f.write("...1cnv.fssp read\n") for i in ["author", "compnd", "database", "header", "nalign", "pdbid", "seqlength", "source"]: f.write('head_rec.%s %s\n' % (i, str(getattr(head_rec,i)))) f.write("\nlen(sum_rec) = %d; head_rec.nalign = %d\n" % (len(sum_rec), head_rec.nalign)) f.write("The above two numbers should be the same\n") f.write("\nCreate a multiple alignment instance using Bio.Align\n") alignment = FSSPTools.mult_align(sum_rec, align_rec) f.write("...Done\n") # Percent ID filtering takes too long.. remove from test. # f.write("\nFilter in percent ID's >= 15%\n") # sum_ge_15, align_ge_15 = FSSPTools.filter(sum_rec, align_rec, 'pID', 15,100) # f.write("\nnumber of records filtered in: %d\n" % len(sum_ge_15)) # k = sum_ge_15.keys() # k.sort()
from Bio import FSSP, Align from Bio.FSSP import FSSPTools import sys import os import cPickle import time test_file = os.path.join('FSSP', '1cnv.fssp') f = sys.stdout f.write("\nRead in %s\n" % os.path.basename(test_file)) head_rec, sum_rec, align_rec = FSSP.read_fssp(open(test_file)) f.write("...1cnv.fssp read\n") for i in ["author", "compnd", "database", "header", "nalign", "pdbid", "seqlength", "source"]: f.write('head_rec.%s %s\n' % (i, str(getattr(head_rec,i)))) f.write("\nlen(sum_rec) = %d; head_rec.nalign = %d\n" % (len(sum_rec), head_rec.nalign)) f.write("The above two numbers should be the same\n") f.write("\nCreate a multiple alignment instance using Bio.Align\n") alignment = FSSPTools.mult_align(sum_rec, align_rec) f.write("...Done\n") # Percent ID filtering takes too long.. remove from test. # f.write("\nFilter in percent ID's >= 15%\n") # sum_ge_15, align_ge_15 = FSSPTools.filter(sum_rec, align_rec, 'pID', 15,100) # f.write("\nnumber of records filtered in: %d\n" % len(sum_ge_15)) # k = sum_ge_15.keys() # k.sort() # f.write("\nRecords filtered in %s\n" % k) # Pickling takes too long.. remove from test.