def test_YDR114C(self): """Maximum number of iterations prevents overlong searches""" pp = self.pp # This sequence takes an eternity to search for pI. pp = protprop.ProteinProperties() ydr = "MPLFARLCQPQSRRMFSSISSFSALSVLRPQTGMLLNSSPLKTPSFTPLGFGLIGQRRWKSRGNTYQPSTLKRKRTFGFLARAKSKQGSKILKRRKLKGRWFLSH" pI = pp.getIsoelectricPoint(ydr) charge = pp.getCharge(ydr, pH=7.2)
def test_comp_counts(self): """Composition and motifs with skips""" comp = protprop.Composition() pp = protprop.ProteinProperties() aa_classes = ['FY','P','NQ'] for xi in range(5): seq = genMotif(aa_classes, [(0,2),(1,1),(2,2),(0,2),(1,1),(2,2)]) counts = pp.counts(seq, aa_classes) self.assertTrue(counts==[4,2,4])
def test_run_skip(self): """Composition and motifs with skips""" comp = protprop.Composition() pp = protprop.ProteinProperties() aa_classes = ['FY','P','NQ'] for xi in range(5): seq = genMotif(aa_classes, [(0,2),(1,1),(2,2),(0,2),(1,1),(2,2)]) self.assertTrue(pp.count(seq, 'FY')==4) mot = pp.motif(seq, ['FY','NQ']) #print seq, mot self.assertTrue(mot=='aabbaabb')
def test_alldistcount(self): """Number of distances for all distances""" comp = protprop.Composition() pp = protprop.ProteinProperties() aa_classes = ['A'] aa = aa_classes[0] for xi in range(2,10): seq = ''.join(aa*xi) #print seq dists = pp.allDistances(seq, aa) self.assertTrue(len(dists[aa])==stats.Choose(xi,2))
def test_neardist(self): """Nearest distances""" comp = protprop.Composition() pp = protprop.ProteinProperties() aa_classes = ['FY','P','NQ'] for xi in range(5): seq = genMotif(aa_classes, [(0,2),(1,1),(2,2),(0,2),(1,1),(2,2)]) #print seq dists = pp.nearestDistances(seq, aa_classes) #print dists hist = stats.Histogram(vals=dists['FY'], n_bins=7, min_val=-0.5,max_val=6.5) #print hist self.assertTrue(hist[1].count==2) self.assertTrue(hist[4].count==1) self.assertTrue(hist[2].count==0)
def test_alldist(self): """All distances""" comp = protprop.Composition() pp = protprop.ProteinProperties() aa_classes = ['FY','P','NQ'] for xi in range(5): seq = genMotif(aa_classes, [(0,2),(1,1),(2,2),(0,2),(1,1),(2,2)]) #print seq dists = pp.allDistances(seq, aa_classes) #print dists hist = stats.Histogram(vals=dists['FY'], n_bins=7, min_val=-0.5,max_val=6.5) #print hist self.assertTrue(hist[1].count==2) self.assertTrue(hist[4].count==1) self.assertTrue(hist[2].count==0) answer = [1, 5, 6, 4, 5, 1] for (a,b) in zip(dists['FY'], answer): self.assertTrue(a==b)
def setUp(self): self.pp = protprop.ProteinProperties()
help="translate the input sequences?")
parser.add_argument("--pH",
dest="pH",
type=float,
default=7.2,
help="pH for charge determination")
options = parser.parse_args()
outs = util.OutStreams()
if not options.out_fname is None:
outf = file(os.path.expanduser(options.out_fname), 'w')
outs.addStream(outf)
else:
outs.addStream(sys.stdout)
pp = protprop.ProteinProperties()
if not options.sequence is None:
if options.translate:
seq = translate.translateRaw(options.sequence)
else:
seq = options.sequence
seq_dict = {"input": seq}
else:
# Load from FASTA
seq_dict = biofile.readFASTADict(options.in_fname)
if options.translate:
for k in seq_dict.keys():
seq_dict[k] = translate.translate(seq_dict[k])
outs.write("# {}\n".format(options))
outs.write("pos\taa\tcharge\n")
def __init__(self):
self._prop = protprop.ProteinProperties()