Python FSSP.read_fssp 예제들

예제 #1

파일: test_FSSP.py 프로젝트: znruss/biopython

# 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.

예제 #2

파일: test_FSSP.py 프로젝트: zyha/biopython

 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()

예제 #3

 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)

예제 #4

파일: test_FSSP.py 프로젝트: davidmam/biopython

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()

예제 #5

파일: test_FSSP.py 프로젝트: Mat-D/biopython

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.