This shows two ways of perturbing the inverse of a distance matrix
so that its rows and columns each end up summing to zero.
"""
from StringIO import StringIO
import numpy as np
from SnippetUtil import HandlingError
import MatrixUtil
import Util
import Form
import FormOut
import const
g_data = const.read('20100730o')
def get_form():
"""
@return: the body of a form
"""
lines = Util.get_stripped_lines(g_data.splitlines())
D = np.array(MatrixUtil.read_matrix(lines))
form_objects = [
Form.Matrix('matrix', 'distance matrix',
D, MatrixUtil.assert_predistance)]
return form_objects
def get_form_out():
return FormOut.Report()
import numpy as np
from scipy import cluster
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import Carbone
import kmeans
import const
import RUtil
g_tags = ['pca:misc']
g_default = const.read('20100709a')
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('table', 'R table', g_default),
Form.Sequence('axes', 'column labels of Euclidean axes',
('pc1', 'pc2', 'pc3')),
Form.CheckGroup(
'options', 'more options',
[Form.CheckItem('verbose', 'show calinski index values', True)])
]
return form_objects
from StringIO import StringIO
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Util
import MatrixUtil
import iterutils
from Form import RadioItem
import Form
import FormOut
import const
g_edge_data = const.read('20100730u')
def get_form():
"""
@return: a list of form objects
"""
# define the edges of the default sparse graph
edge_lines = Util.get_stripped_lines(g_edge_data.splitlines())
# define the vertices to be removed by default
vertices_to_be_removed = ['A', 'a']
# define the list of form objects
form_objects = [
Form.MultiLine('graph', 'sparse graph with edge weights',
'\n'.join(edge_lines)),
Form.MultiLine('vertices', 'vertices to be removed',
'\n'.join(vertices_to_be_removed)),
"""
from StringIO import StringIO
import numpy as np
from SnippetUtil import HandlingError
import Form
import FormOut
import MatrixUtil
import NewickIO
import FelTree
import HtmlTable
import const
g_default_string = const.read("20100730q")
# FIXME use library functions
def get_form():
"""
@return: a list of form objects
"""
# define the default tree string
tree = NewickIO.parse(g_default_string, FelTree.NewickTree)
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# return the form objects
form_objects = [Form.MultiLine("tree", "newick tree with branch lengths", formatted_tree_string)]
return form_objects
from scipy import linalg
import numpy as np
import cairo
from SnippetUtil import HandlingError
import SnippetUtil
import Form
import FormOut
import CairoUtil
import MatrixUtil
import Clustering
import NewickIO
import FelTree
import const
g_default_string = const.read('20100730q')
def get_form():
"""
@return: a list of form objects
"""
tree = NewickIO.parse(g_default_string, FelTree.NewickTree)
formatted_default_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# define the list of form objects
form_objects = [
Form.MultiLine('tree', 'tree', formatted_default_tree_string),
Form.CheckGroup(
'processing_options', 'processing options',
[Form.CheckItem('internal', 'process internal nodes', True)]),
Form.CheckGroup('visualization_options', 'visualization options', [
"""Sort the names in a non-interleaved phylip alignment.
"""
from SnippetUtil import HandlingError
import Form
import FormOut
import Phylip
import const
g_tags = ['pca:misc']
g_default_data = const.read('20100625a')
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('phylip', 'non-interleaved Phylip alignment',
g_default_data)
]
return form_objects
def get_form_out():
return FormOut.Phylip()
def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
import numpy as np
from scipy import cluster
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import Carbone
import kmeans
import const
import RUtil
g_tags = ['pca:misc']
g_default = const.read('20100709a')
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('table', 'R table', g_default),
Form.Sequence('axes', 'column labels of Euclidean axes',
('pc1', 'pc2', 'pc3')),
Form.CheckGroup('options', 'more options', [
Form.CheckItem('verbose',
'show calinski index values', True)])]
return form_objects
def get_form_out():
"""Given a newick tree, calculate weights for a subset of the tips.
"""
from SnippetUtil import HandlingError
import Newick
import LeafWeights
import Util
from Form import RadioItem
import Form
import FormOut
import const
g_ucsc_tree_string = const.read('20100730x')
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = g_ucsc_tree_string
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# default name selection
default_name_selection = ('human_hg18', 'chimp_panTro1', 'rabbit_oryCun1')
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('selection', 'selected tip names',
'\n'.join(default_name_selection)),
Form.RadioGroup('method', 'weighting method', [
RadioItem('stone', 'use the method of Stone and Sidow', True),
import os
import cairo
import numpy as np
from SnippetUtil import HandlingError
import Form
import FormOut
import CairoUtil
import Euclid
import BuildTreeTopology
import SchurAlgebra
import Util
import const
g_data = const.read('20100125a')
def get_default_data():
lines = Util.get_stripped_lines(g_data.splitlines())
return '\n'.join(lines)
class BorderInfo:
def __init__(self, border_x, border_y):
self.border_x = border_x
self.border_y = border_y
class AxisInfo:
def __init__(self, flip_x, flip_y, show_x, show_y):
self.flip_x = flip_x
self.flip_y = flip_y
self.show_x = show_x
"""
from StringIO import StringIO
import argparse
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import RUtil
import Carbone
import const
g_tags = ['pca:compute']
g_table = const.read('20100920a')
g_factor = 'cluster'
g_variable = 'temperature'
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('table', 'R table', g_table),
Form.SingleLine('factor', 'factor name', g_factor),
Form.SingleLine('variable', 'variable name', g_variable)]
return form_objects
import argparse
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Form
import FormOut
import NewickIO
import FelTree
import Euclid
import TreeSampler
import Util
import const
g_D_abdi = const.read('20100730h')
def get_form():
"""
@return: a list of form objects
"""
# define the list of form objects
form_objects = []
return form_objects
def get_form_out():
return FormOut.Report()
def process():
"""
@return: a multi-line string that summarizes the results
MAPP stands for Multivariate Analysis of Protein Polymorphism.
"""
from StringIO import StringIO
from SnippetUtil import HandlingError
import SnippetUtil
import Newick
import Codon
import Util
import Form
import FormOut
import const
g_mapp_output = const.read('20100730v')
class ColumnDataError(Exception):
pass
class ColumnData:
"""
Define data associated with the column of an alignment.
"""
def __init__(self, gene, offset, wild, mutant):
"""
@param gene: the name of a gene
@param offset: the integer offset indexed starting at 1
for Functional Genomic Inference".
"""
import math
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Form
import FormOut
import Util
import MatrixUtil
import const
g_karate_data = const.read("20090406a")
def get_form():
"""
@return: the body of a form
"""
# define the default observation lines
default_observation_matrix = [
["Gene/Observation", "Observation 1", "Observation 2", "Observation 3", "Observation 4", "Observation 5"],
["Gene 1", "4.1", "6.23", "3.141529", "8.008", "1.2"],
["Gene 2", "1.3", "7", "8.12", "1.1", "9.321"],
["Gene 3", "6.21", "9.001", "3.76", "6.18", "5"],
]
default_observation_lines = [",\t".join(row) for row in default_observation_matrix]
# define the default module lines
"""
import numpy as np
from SnippetUtil import HandlingError
import Util
import MatrixUtil
import Clustering
import NeighborhoodJoining
import NewickIO
import Form
import FormOut
import const
# this is a perturbed distance matrix not an exact distance matrix
g_d = const.read('20100730p')
def get_form():
"""
@return: the body of a form
"""
lines = Util.get_stripped_lines(g_d.splitlines())
D = np.array(MatrixUtil.read_matrix(lines))
labels = list('xyabcmnp')
# define the form objects
form_objects = [
Form.Matrix('matrix', 'distance matrix',
D, MatrixUtil.assert_predistance),
Form.MultiLine('labels', 'ordered labels',
'\n'.join(labels)),
Form.RadioGroup('recourse', 'recourse for degenerate partitions', [
"Maximum Likelihood Phylogenetic Estimation from DNA Sequences
with Variable Rates over Sites: Approximate Methods"
by Ziheng Yang in J Mol Evol 1994.
"""
from StringIO import StringIO
from SnippetUtil import HandlingError
import Fasta
import F84
import PairLikelihood
import Form
import FormOut
import const
g_sample_fasta_string = const.read('20100730z')
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('fasta', 'nucleotide sequence pair',
g_sample_fasta_string.strip())
]
return form_objects
def get_form_out():
return FormOut.Report()
"""
from StringIO import StringIO
import time
import itertools
import optparse
import random
from SnippetUtil import HandlingError
import Util
import Form
import FormOut
import Progress
import const
g_raw_matrix = const.read('20100730l').rstrip()
def get_hamming_distance(a, b):
"""
@param a: a sequence of ones and zeros
@param b: a sequence of ones and zeros
@return: the hamming distance
"""
return Util.hamming_distance(a, b)
def get_folded_distance(a, b):
"""
@param a: a sequence of ones and zeros
@param b: a sequence of ones and zeros
@return: a distance
"""
from SnippetUtil import HandlingError
import FelTree
import NewickIO
import Codon
import Fasta
import Util
import iterutils
import Form
import FormOut
import const
# TODO de-hardcode this path to the jar file
g_mapp_jar_path = '/home/argriffi/mapp-analysis/MAPP.jar'
g_default_csv_data = const.read('20100730t')
g_default_tree_string = const.read('20100730s')
def get_form():
"""
@return: a list of form objects
"""
default_tree_string = '(a:2, b:2, (c:2, d:2):2);'
form_objects = [
Form.MultiLine('data', 'raw data from a csv file',
g_default_csv_data),
Form.MultiLine('tree', 'a tree with branch lengths',
g_default_tree_string)]
return form_objects
import hmmus
import scipy.misc
from SnippetUtil import HandlingError
import Form
import FormOut
import DGRP
import ReadCoverageRef
import Util
import ExternalHMM
import lineario
import TransitionMatrix
import const
g_default_data = const.read('20100729a')
g_default_params = [('x', '0.1'), ('y', '0.01'), ('z', '0.0001'), ('low', '2'),
('med', '20'), ('high', '1000'), ('seqerr', '.01'),
('nomcoverage', '20'), ('kmulticoverages', '4')]
def get_form():
"""
@return: the body of a form
"""
data_lines = ['\t'.join(str(x) for x in row) for row in g_default_data]
form_objects = [
Form.Integer('region_size',
'expected region size',
10,
from StringIO import StringIO
import math
from math import sqrt
import numpy as np
import scipy
from scipy import interpolate
from scipy import optimize
import Form
import FormOut
import Util
import const
g_tw1_csv = const.read('20120505a')
g_m = 189
g_n = 2790
g_eigenvalues = """
22.36
8.20
5.09
3.81
3.33
2.09
1.89
1.44
1.30
import math
import os
import cairo
import numpy as np
from SnippetUtil import HandlingError
import Form
import FormOut
import CairoUtil
import Euclid
import BuildTreeTopology
import Util
import const
g_data = const.read('20100125a')
def get_default_data():
lines = Util.get_stripped_lines(g_data.splitlines())
return '\n'.join(lines)
class BorderInfo:
def __init__(self, border_x, border_y):
self.border_x = border_x
self.border_y = border_y
class AxisInfo:
def __init__(self, flip_x, flip_y, show_x, show_y):
self.flip_x = flip_x
self.flip_y = flip_y
self.show_x = show_x
P: internal vertex principal submatrix (symmetric order p)
X: off-diagonal upper right submatrix (pxq or qxp)
"""
import unittest
import numpy as np
import NewickIO
import MatrixUtil
import EigUtil
import FelTree
import iterutils
import const
g_tree_string = const.read('20100730g').rstrip()
############################################################
# block matrix helper functions
def hrep(M, N):
"""
Horizontally stack N copies of M.
@param M: a matrix
@param N: stack this many copies
"""
return np.hstack([M]*N)
def vrep(M, N):
"""
import hmmus
import scipy.misc
from SnippetUtil import HandlingError
import Form
import FormOut
import DGRP
import ReadCoverageRef
import Util
import ExternalHMM
import lineario
import TransitionMatrix
import const
g_default_data = const.read('20100729a')
g_default_params = [
('x', '0.1'),
('y', '0.01'),
('z', '0.0001'),
('low', '2'),
('med', '20'),
('high', '1000'),
('seqerr', '.01'),
('nomcoverage', '20'),
('kmulticoverages', '4')]
def get_form():
"""
@return: the body of a form
For example, this can be used for a city MDS plot.
"""
from StringIO import StringIO
import math
import cairo
from SnippetUtil import HandlingError
import Form
import FormOut
import CairoUtil
import Util
import const
g_default_data = const.read('20100730d')
class BorderInfo:
def __init__(self, border_x, border_y):
self.border_x = border_x
self.border_y = border_y
class AxisInfo:
def __init__(self, flip_x, flip_y, show_x, show_y):
self.flip_x = flip_x
self.flip_y = flip_y
self.show_x = show_x
self.show_y = show_y
class ImageInfo:
import numpy as np
import scipy
import Form
import FormOut
import tikz
import latexutil
import Ftree
import FtreeIO
import FtreeAux
import MatrixUtil
import Newick
import const
g_tree_string = const.read('20110616a').rstrip()
def get_form():
"""
@return: a list of form objects
"""
# reformat the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree',
formatted_tree_string),
Form.Float('scaling_factor',
'figure scaling factor', 3.0, low_exclusive=0),
import sys
import numpy as np
from SnippetUtil import HandlingError
import Form
import FormOut
import Progress
import TransitionMatrix
import ReadCoverage
import FastHMM
import iterutils
import Util
import const
g_sample_data = const.read('20100730j')
class TimeoutError(Exception): pass
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.Integer('good_coverage',
'expected read coverage of informative positions',
20, low=1, high=1000),
Form.Integer('bad_coverage',
'expected read coverage of overcovered positions',
100, low=1, high=1000),
Form.Integer('nstickinesses',
"""Remove root branch length and internal labels from a tree, and unroot it.
"""
from StringIO import StringIO
import os
from SnippetUtil import HandlingError
import Form
import FormOut
import NewickIO
import FelTree
import Newick
import BuildTreeTopology
import const
g_tree_data = const.read('20090802d')
def get_form():
"""
@return: the body of a form
"""
# define the formatted tree string
tree = NewickIO.parse(g_tree_data, Newick.NewickTree)
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# return the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string)
]
return form_objects
import math
import cairo
import numpy as np
from SnippetUtil import HandlingError
import Codon
import Form
import FormOut
import CairoUtil
import Util
import Euclid
import BuildTreeTopology
import const
g_default_data = const.read('20100730e')
class ImageInfo:
def __init__(self, total_width, total_height, border, image_format):
"""
@param total_width: total image width in pixels
@param total_height: total image height in pixels
@param border: image border size in pixels
@param image_format: image format
"""
self.total_width = total_width
self.total_height = total_height
self.border = border
self.image_format = image_format
if self.get_drawable_width() < 1 or self.get_drawable_height < 1:
from scipy import optimize
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Fasta
import MatrixUtil
import RateMatrix
import Util
import PairLikelihood
import Form
import FormOut
import const
g_fasta = const.read('20100730y')
class Objective:
def __init__(self, sequence_pair, rate_matrix):
"""
@param sequence_pair: a pair of sequences
@param rate_matrix: a rate matrix object
"""
self.rate_matrix = rate_matrix
self.sequence_pair = sequence_pair
def __call__(self, branch_length):
"""
This will be called by a one dimensional minimizer.
@param branch_length: the distance between the two aligned sequences
from StringIO import StringIO
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Util
import MatrixUtil
import Euclid
import SchurAlgebra
import Form
import FormOut
import const
g_data = const.read('20100730p')
def get_form():
"""
@return: the body of a form
"""
# define the default distance matrix
# this is from figure two of a paper called why neighbor joining works
D = MatrixUtil.read_matrix(Util.get_stripped_lines(g_data.splitlines()))
states = list('xyabcmnp')
# define some default strings
ordered_label_string = '\n'.join(states)
selected_label_string = '\n'.join(['m', 'n'])
# define the sequence of form objects
form_objects = [
Form.Matrix('matrix', 'distance matrix',
from StringIO import StringIO
import math
import numpy as np
from SnippetUtil import HandlingError
import Form
import FormOut
import NewickIO
import Euclid
import FelTree
import SchurAlgebra
import EigUtil
import const
g_tree_string = const.read("20100730g").rstrip()
def get_form():
"""
@return: a list of form objects
"""
# define the form objects
form_objects = [
Form.MultiLine("tree_string", "newick tree", g_tree_string),
Form.Float("strength", "duplicate node pair connection strength", 100),
]
return form_objects
def get_form_out():
"""
from StringIO import StringIO
import argparse
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import RUtil
import Carbone
import const
g_tags = ['pca:compute']
g_table = const.read('20100709a')
g_independent_names = ['temperature', 'precipitation']
g_dependent_name = 'pc1'
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('table', 'R table', g_table),
Form.MultiLine('independent', 'names of independent variables',
'\n'.join(g_independent_names)),
Form.SingleLine('dependent', 'name of the dependent variable',
for Functional Genomic Inference".
"""
import math
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Form
import FormOut
import Util
import MatrixUtil
import const
g_karate_data = const.read('20090406a')
def get_form():
"""
@return: the body of a form
"""
# define the default observation lines
default_observation_matrix = [[
'Gene/Observation', 'Observation 1', 'Observation 2', 'Observation 3',
'Observation 4', 'Observation 5'
], ['Gene 1', '4.1', '6.23', '3.141529', '8.008',
'1.2'], ['Gene 2', '1.3', '7', '8.12', '1.1',
'9.321'], ['Gene 3', '6.21', '9.001', '3.76', '6.18', '5']]
default_observation_lines = [
',\t'.join(row) for row in default_observation_matrix
"""Sort the names in a non-interleaved phylip alignment.
"""
from SnippetUtil import HandlingError
import Form
import FormOut
import Phylip
import const
g_tags = ['pca:misc']
g_default_data = const.read('20100625a')
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('phylip', 'non-interleaved Phylip alignment',
g_default_data)]
return form_objects
def get_form_out():
return FormOut.Phylip()
def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
new_pairs = sorted(zip(headers, sequences))
new_headers, new_sequences = zip(*new_pairs)
return Phylip.encode(new_headers, new_sequences) + '\n'
import os
import colorsys
import argparse
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import RUtil
import Carbone
import iterutils
import const
g_tags = ["pca:plot"]
g_default = const.read("20100709a")
g_colorbrewer_set1 = ["#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999"]
# FIXME multiple output types
def rgb_floats_to_ints(rgb_floats):
return tuple(int(round(x * 255)) for x in rgb_floats)
def create_R_palette(n):
"""
@param n: make a list of this many colors
@return: a list of R colors like #E41A1C
"""
from StringIO import StringIO
import os
import math
import numpy as np
from SnippetUtil import HandlingError
import SnippetUtil
import Util
import Form
import FormOut
import GPS
import Euclid
import const
g_mds_data = const.read('20100119b')
def parse_lines(lines):
"""
The input lines have a special format.
The first nonempty line is a header.
The subsequent lines are whitespace separated values.
The first value is the city name.
The next four values are latitude and longitude minutes and degrees.
@param lines: stripped input lines
@return: (city, lat_deg, lat_min, lon_deg, lon_min) tuples
"""
lines = [line for line in lines if line]
if not lines:
raise HandlingError('no input was found')
from StringIO import StringIO
import math
from math import sqrt
import numpy as np
import scipy
from scipy import interpolate
from scipy import optimize
import Form
import FormOut
import Util
import const
g_tw1_csv = const.read('20120505a')
g_m = 189
g_n = 2790
g_eigenvalues = """
22.36
8.20
5.09
3.81
3.33
2.09
1.89
1.44
1.30
corresponding to positions not represented in the input file)
will have undefined count entries.
They will probably be arbitrarily set to zero, but should be ignored.
The input file should represent a single chromosome and a single strain.
"""
from StringIO import StringIO
import optparse
import sys
from SnippetUtil import HandlingError
import Form
import FormOut
import const
g_sample_input = const.read('20100730i')
class LineLimitError(Exception): pass
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('multiline_input',
'input file lines', g_sample_input)]
return form_objects
def get_form_out():
return FormOut.Report()
from StringIO import StringIO
import numpy as np
import scipy
import Form
import FormOut
import Ftree
import FtreeIO
import MatrixUtil
import Newick
import forest
import const
g_tree_string = const.read('20110616a').rstrip()
def get_form():
"""
@return: a list of form objects
"""
# reformat the tree string
tree = Newick.parse(g_tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 75)
# define the form objects
form_objects = [
Form.MultiLine('tree_string', 'newick tree', formatted_tree_string)
]
return form_objects
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import FelTree
import Newick
import NewickIO
import MatrixUtil
import HtmlTable
import MAPP
import Codon
import LeafWeights
import const
g_annotation_data = const.read('20100526a')
g_tree_data = const.read('20100526b')
# TODO de-hardcode this path to the jar file
g_mapp_jar_path = '/home/argriffi/mapp-analysis/MAPP.jar'
g_ordered_taxon_names = [
'hg18', 'rheMac2', 'mm9', 'canFam2', 'loxAfr2', 'monDom4', 'ornAna1',
'galGal3', 'anoCar1', 'xenTro2', 'gasAcu1'
]
g_unordered_taxon_names = set(g_ordered_taxon_names)
def get_reverse_complement(s):
trans = {'A': 'T', 'T': 'A', 'C': 'G', 'G': 'C'}
"""Given a newick tree, calculate weights for a subset of the tips.
"""
from SnippetUtil import HandlingError
import Newick
import LeafWeights
import Util
from Form import RadioItem
import Form
import FormOut
import const
g_ucsc_tree_string = const.read('20100730x')
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree_string = g_ucsc_tree_string
tree = Newick.parse(tree_string, Newick.NewickTree)
formatted_tree_string = Newick.get_narrow_newick_string(tree, 60)
# default name selection
default_name_selection = ('human_hg18', 'chimp_panTro1', 'rabbit_oryCun1')
# define the form objects
form_objects = [
Form.MultiLine('tree', 'newick tree', formatted_tree_string),
Form.MultiLine('selection', 'selected tip names',
'\n'.join(default_name_selection)),
Form.RadioGroup('method', 'weighting method', [
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import FelTree
import Newick
import NewickIO
import MatrixUtil
import HtmlTable
import MAPP
import Codon
import LeafWeights
import const
g_annotation_data = const.read('20100526a')
g_tree_data = const.read('20100526b')
# TODO de-hardcode this path to the jar file
g_mapp_jar_path = '/home/argriffi/mapp-analysis/MAPP.jar'
g_ordered_taxon_names = [
'hg18',
'rheMac2',
'mm9',
'canFam2',
'loxAfr2',
'monDom4',
'ornAna1',
'galGal3',
'anoCar1',
between pairs of aligned sequences using JC69.
The rows and columns of the output distance matrix
are ordered according to the sequence order in the alignment.
The likelihood maximization can be done analytically
because of the simplicity of the model.
"""
from SnippetUtil import HandlingError
import Fasta
import MatrixUtil
import JC69
import Form
import FormOut
import const
g_fasta = const.read('20100730y')
def get_form():
"""
@return: the body of a form
"""
# define the form objects
form_objects = [
Form.MultiLine('fasta', 'aligned sequences without gaps',
g_fasta.strip()),
Form.Float('infinity', 'use this value for estimates of infinity',
100.0)]
return form_objects
def get_form_out():
return FormOut.Matrix()
import numpy as np
from SnippetUtil import HandlingError
import RateMatrix
import Newick
import Monospace
import HeatMap
import Fasta
import SubModel
import iterutils
import Form
import FormOut
import const
g_sample_alignment_string = const.read('20100731c')
g_nt_matrix_a = np.array([[-3, 1, 1, 1], [1, -3, 1, 1], [1, 1, -3, 1],
[1, 1, 1, -3]])
g_nt_matrix_b = np.array([[-3, 1, 1, 1], [1, -3, 1, 1], [1, 1, -3, 1],
[1, 1, 1, -3]])
g_nt_matrix_c = np.array([[-3, 1, 1, 1], [10, -12, 1, 1], [10, 1, -12, 1],
[10, 1, 1, -12]])
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
import os
import subprocess
import argparse
import numpy as np
import Form
import FormOut
import const
import mcmc
import Util
import Fasta
import RUtil
g_fasta_string = const.read('20120405a').strip()
g_ntax = 12
g_nchar = 898
g_beast_root = os.path.expanduser('~/svn-repos/beast-mcmc-read-only')
g_headers = (
'sequence.length',
'mean.low', 'mean.mean', 'mean.high',
'var.low', 'var.mean', 'var.high',
'cov.low' ,'cov.mean', 'cov.high')
#TODO use lxml
#TODO use the beastut and beast modules
g_xml_pre_alignment = """
from enthought.mayavi import mlab
import numpy as np
from StringIO import StringIO
import math
from itertools import product
import NewickIO
import Euclid
import MatrixUtil
import EigUtil
import FelTree
import ProofDecoration
import const
g_tree_string = const.read('20100730g').rstrip()
g_plane_opacity = 0.1
g_crossing_opacity = 1.0
g_crossing_radius = 0.1
def add_yz_plane():
x = [0, 0, 0, 0]
y = [-1, -1, 1, 1]
z = [-1, 1, 1, -1]
tris = [(0, 3, 2), (2, 1, 0)]
mesh = mlab.triangular_mesh(x,
y,
z,
tris,
import math
from StringIO import StringIO
import cairo
from SnippetUtil import HandlingError
import SnippetUtil
import Newick
import CairoUtil
import Codon
import Util
import Form
import FormOut
import const
g_mapp_output = const.read('20100730v')
class ColumnDataError(Exception):
pass
class ColumnData:
"""
Define data associated with the column of an alignment.
"""
def __init__(self, gene, offset, wild, mutant):
"""
@param gene: the name of a gene
@param offset: the integer offset indexed starting at 1
by Ziheng Yang in J Mol Evol 1994.
"""
from StringIO import StringIO
import scipy.optimize
from SnippetUtil import HandlingError
import Fasta
import F84
import PairLikelihood
import Form
import FormOut
import const
g_sample_fasta_string = const.read('20100730z')
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine('fasta', 'nucleotide sequence pair',
g_sample_fasta_string.strip())]
return form_objects
def get_form_out():
return FormOut.Report()
def get_response_content(fs):
# get the alignment object
"""
from StringIO import StringIO
import random
import os
import subprocess
import multiprocessing
from multiprocessing import Pool
import const
import mcmc
import Fasta
import RUtil
import Util
g_fasta_string = const.read('20120405a').strip()
g_nchar = 898
g_beast_root = os.path.expanduser('~/svn-repos/beast-mcmc-read-only')
g_headers = ('sequence.length', 'midpoint', 'mean.low', 'mean.mean',
'mean.high', 'var.low', 'var.mean', 'var.high', 'cov.low',
'cov.mean', 'cov.high')
g_xml_pre_alignment = """
<?xml version="1.0" standalone="yes"?>
<beast>
<!-- The list of taxa analyse (can also include dates/ages). -->
<taxa id="taxa">
<taxon id="Tarsius_syrichta"/>
<taxon id="Lemur_catta"/>
<taxon id="Homo_sapiens"/>
"""
from StringIO import StringIO
import numpy as np
from SnippetUtil import HandlingError
import MatrixUtil
import Form
import FormOut
import NewickIO
import FelTree
import Clustering
import const
g_default_string = const.read('20100730m')
def get_form():
"""
@return: the body of a form
"""
# define the default tree string
tree = NewickIO.parse(g_default_string, FelTree.NewickTree)
formatted_tree_string = NewickIO.get_narrow_newick_string(tree, 60)
# define the form objects
form_objects = [
Form.MultiLine('tree',
'newick tree with branch lengths', formatted_tree_string),
Form.SingleLine('lhs_a',
'the first taxon on one side of the split', 'a'),
Form.SingleLine('lhs_b',
"""
import numpy as np
from SnippetUtil import HandlingError
import Util
import MatrixUtil
import Clustering
import NeighborhoodJoining
import NewickIO
import Form
import FormOut
import const
# this is a perturbed distance matrix not an exact distance matrix
g_d = const.read('20100730p')
def get_form():
"""
@return: the body of a form
"""
lines = Util.get_stripped_lines(g_d.splitlines())
D = np.array(MatrixUtil.read_matrix(lines))
labels = list('xyabcmnp')
# define the form objects
form_objects = [
Form.Matrix('matrix', 'distance matrix', D,
MatrixUtil.assert_predistance),
Form.MultiLine('labels', 'ordered labels', '\n'.join(labels)),
Form.RadioGroup('recourse', 'recourse for degenerate partitions', [
The number of MCMC steps is also set.
The web interface modifies the primates.xml from the BEAST tutorial.
"""
from StringIO import StringIO
import argparse
import sys
from lxml import etree
import Form
import FormOut
import const
g_primates_xml = const.read('20120605a')
def get_form():
form_objects = [
Form.IntegerInterval(
'start_pos', 'stop_pos', 'alignment interval',
1, 4263, low=1, high=4263),
Form.Integer('nsteps', 'MCMC steps', 8000, low=1),
Form.SingleLine('alignment_id', 'alignment id', 'alignment'),
Form.SingleLine('mcmc_id', 'mcmc id', 'mcmc'),
]
return form_objects
def get_form_out():
return FormOut.BeastXml()
import NewickIO
import FelTree
import Newick
import BuildTreeTopology
import SchurAlgebra
import Euclid
import MatrixUtil
from Form import CheckGroup
from Form import CheckItem
from Form import RadioGroup
from Form import RadioItem
import Form
import FormOut
import const
g_archaea_data = const.read('20090802a')
g_bacteria_data = const.read('20090802b')
g_eukaryota_data = const.read('20090802c')
g_full_data = const.read('20090802d')
g_valid_domains = set(['archaea', 'bacteria', 'eukaryota'])
#FIXME multiple output types
def get_form():
"""
@return: the body of a form
"""
form_objects = [
RadioGroup('distance_options', 'recursive matrix construction', [
import numpy as np
from SnippetUtil import HandlingError
import RateMatrix
import Newick
import Monospace
import HeatMap
import Fasta
import SubModel
import iterutils
import Form
import FormOut
import const
g_sample_alignment_string = const.read('20100731c')
g_nt_matrix_a = np.array([
[-3, 1, 1, 1], [1, -3, 1, 1], [1, 1, -3, 1], [1, 1, 1, -3]])
g_nt_matrix_b = np.array([
[-3, 1, 1, 1], [1, -3, 1, 1], [1, 1, -3, 1], [1, 1, 1, -3]])
g_nt_matrix_c = np.array([
[-3, 1, 1, 1], [10, -12, 1, 1], [10, 1, -12, 1], [10, 1, 1, -12]])
def get_form():
"""
@return: the body of a form
"""
# define the tree string
tree_string = '(((Human:0.1, Chimpanzee:0.2):0.8, Gorilla:0.3):0.7, Orangutan:0.4, Gibbon:0.5);'
tree = Newick.parse(tree_string, Newick.NewickTree)
from SnippetUtil import HandlingError
import FelTree
import NewickIO
import Codon
import Fasta
import Util
import iterutils
import Form
import FormOut
import const
# TODO de-hardcode this path to the jar file
g_mapp_jar_path = '/home/argriffi/mapp-analysis/MAPP.jar'
g_default_csv_data = const.read('20100730t')
g_default_tree_string = const.read('20100730s')
def get_form():
"""
@return: a list of form objects
"""
default_tree_string = '(a:2, b:2, (c:2, d:2):2);'
form_objects = [
Form.MultiLine('data', 'raw data from a csv file', g_default_csv_data),
Form.MultiLine('tree', 'a tree with branch lengths',
g_default_tree_string)
]
return form_objects
"""
from StringIO import StringIO
import argparse
from SnippetUtil import HandlingError
import Form
import FormOut
import Util
import RUtil
import Carbone
import const
g_tags = ["pca:compute"]
g_table = const.read("20100709a")
g_independent_names = ["temperature", "precipitation"]
g_dependent_name = "pc1"
def get_form():
"""
@return: the body of a form
"""
form_objects = [
Form.MultiLine("table", "R table", g_table),
Form.MultiLine("independent", "names of independent variables", "\n".join(g_independent_names)),
Form.SingleLine("dependent", "name of the dependent variable", g_dependent_name),
]
from StringIO import StringIO
from scipy import optimize
import numpy as np
from SnippetUtil import HandlingError
import Fasta
import MatrixUtil
import RateMatrix
import Util
import PairLikelihood
import Form
import FormOut
import const
g_fasta = const.read('20100731a')
def get_form():
"""
@return: the body of a form
"""
# define the default matrix
# HKY simulation parameters are
# transition/transversion ratio 2, C:4, G:4, A:1, T:1
R = np.array([
[-1.3, 0.4, 0.8, 0.1],
[0.1, -0.7, 0.4, 0.2],
[0.2, 0.4, -0.7, 0.1],
[0.1, 0.8, 0.4, -1.3]])
# define the form objects
form_objects = [