Did I find the right examples for you? yes no

All Samples(16)  |  Call(8)  |  Derive(0)  |  Import(8)

src/c/o/cogent-1.5.3/cogent/maths/stats/cai/adaptor.py   cogent(Download)
#/usr/bin/env python
"""Adaptors to fit data read from CUTG or fasta-format files into CAI graphs.
"""
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.core.info import Info
def consolidate(usages):
    """Sums frequencies of a list of usages into one usage."""
    result = CodonUsage()
    for u in usages:
        result += u
            else:
                curr_info['Description'] = ' '.join(fields[1:])
        curr_codon_usage = CodonUsage(seq_to_codon_dict(seq), Info=curr_info)
        curr_codon_usage.__dict__.update(curr_info)
        result.append(curr_codon_usage)
    normalize:      ensure the frequencies returned sum to 1 (True)
    """
    tot_codon_usage = CodonUsage()
    for idx, c in enumerate(codon_usages):
        tot_codon_usage += c
            continue
        try:
            tot_usage = CodonUsage()
            for c in bin:
                tot_usage += c

src/p/y/pycogent-HEAD/cogent/maths/stats/cai/adaptor.py   pycogent(Download)
#/usr/bin/env python
"""Adaptors to fit data read from CUTG or fasta-format files into CAI graphs.
"""
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.core.info import Info
def consolidate(usages):
    """Sums frequencies of a list of usages into one usage."""
    result = CodonUsage()
    for u in usages:
        result += u
            else:
                curr_info['Description'] = ' '.join(fields[1:])
        curr_codon_usage = CodonUsage(seq_to_codon_dict(seq), Info=curr_info)
        curr_codon_usage.__dict__.update(curr_info)
        result.append(curr_codon_usage)
    normalize:      ensure the frequencies returned sum to 1 (True)
    """
    tot_codon_usage = CodonUsage()
    for idx, c in enumerate(codon_usages):
        tot_codon_usage += c
            continue
        try:
            tot_usage = CodonUsage()
            for c in bin:
                tot_usage += c

src/c/o/cogent-1.5.3/cogent/maths/stats/cai/get_by_cai.py   cogent(Download)
#!/usr/bin/env python
"""Produces data that matches the CAI for a gene against its P3."""
from cogent.parse.cutg import CutgParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.usage import UnsafeCodonUsage as CodonUsage, \

src/p/y/pycogent-HEAD/cogent/maths/stats/cai/get_by_cai.py   pycogent(Download)
#!/usr/bin/env python
"""Produces data that matches the CAI for a gene against its P3."""
from cogent.parse.cutg import CutgParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.core.usage import UnsafeCodonUsage as CodonUsage, \

src/c/o/cogent-1.5.3/cogent/draw/util.py   cogent(Download)
    Image = ImageFilter = None  #only used to smooth contours: skip if no PIL
from numpy import array, shape, fromstring, sqrt, zeros, pi
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.maths.stats.test import regress, correlation
from pylab import plot, cm, savefig, gca, gcf, arange, text, subplot, \

src/c/o/cogent-1.5.3/cogent/draw/codon_usage.py   cogent(Download)
rc('text', usetex=True)
rc('font', family='serif')  #required to match latex text and equations
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.draw.util import scatter_classic, \
   init_graph_display, init_ticks, set_axis_to_probs, \

src/p/y/pycogent-HEAD/cogent/draw/util.py   pycogent(Download)
    Image = ImageFilter = None  #only used to smooth contours: skip if no PIL
from numpy import array, shape, fromstring, sqrt, zeros, pi
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.maths.stats.test import regress, correlation
from pylab import plot, cm, savefig, gca, gcf, arange, text, subplot, \

src/p/y/pycogent-HEAD/cogent/draw/codon_usage.py   pycogent(Download)
rc('text', usetex=True)
rc('font', family='serif')  #required to match latex text and equations
from cogent.core.usage import UnsafeCodonUsage as CodonUsage
from cogent.draw.util import scatter_classic, \
   init_graph_display, init_ticks, set_axis_to_probs, \