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'''
This is a python implementation of the Quikr program.
'''
__author__ = "Calvin Morrison"
__credits__ = ["Calvin Morrison", "Gail Rosen", "Simon Foucart", "Jean-Luc Bouchot", "David Koslicki"]
__license__ = "GPL"
__maintainer__ = "Gail Rosen"
__email__ = "gailro@gmail.com"
__status__ = "Release"
import os
import sys
from StringIO import StringIO
import scipy.optimize.nnls
import scipy.sparse
import numpy as np
from subprocess import *
import gzip
import itertools
def is_compressed(filename):
""" This is a helper function to see if a file is gzipped
>>> boolean_value = is_compressed("/path/to/compressed/gzip/file")
>>> print boolean_value
True
input: filename
output: boolean
"""
try:
f = open(filename, "rb")
except IOError:
print "Warning: is_compressed could not find " + filename
return False
# The first two bytes of a gzipped file are always '1f 8b'
if f.read(2) == '\x1f\x8b':
f.close()
return True
else:
f.close()
return False
def train_matrix(input_file_location, kmer):
"""
Takes a input fasta file, and kmer, returns a custom sensing matrix
returns an ndarray
"""
input_file = Popen(["bash", "-c", "probabilities-by-read " + str(kmer) + " " + input_file_location + " <(generate_kmers 6)"], stdout=PIPE)
# load and normalize the matrix by dividing each element by the sum of it's column.
# also do some fancy rotations so that it works properly with quikr
matrix = np.loadtxt(input_file.stdout)
matrix = np.rot90(matrix)
matrix = matrix / matrix.sum(0)
matrix = np.flipud(matrix);
return matrix
def load_sensing_matrix_from_file(sensing_matrix_location):
""" This is a helper function to load our sensing matrix and run quikr """
if is_compressed(sensing_matrix_location):
sensing_matrix_file = gzip.open(sensing_matrix_location, "rb")
else:
sensing_matrix_file = open(sensing_matrix_location, "rb")
sensing_matrix = np.load(sensing_matrix_file)
return sensing_matrix
def calculate_estimated_frequencies(input_fasta_location, sensing_matrix, kmer, default_lambda):
"""
input_fasta is the input fasta file to find the estimated frequencies of
sensing_matrix is the sensing matrix we are using to estimate the species
kmer is the desired k-mer to use
default_lambda is inp
returns the estimated requencies of bacteria present when given an input
FASTA file of amplicon (454) reads. A k-mer based, L1 regularized, sparsity
promoting algorthim is utilized.
In practice reconstruction is accurate only down to the genus level (not
species or strain).
"""
# We use the count program to count
count_input = Popen(["count-kmers", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE)
# load the output of our count program and form a probability vector from the counts
counts = np.loadtxt(count_input.stdout)
counts = counts / counts.sum(0)
counts = default_lambda * counts
counts = np.concatenate([np.zeros(1), counts])
#form the k-mer sensing matrix
sensing_matrix = sensing_matrix * default_lambda;
sensing_matrix = np.vstack((np.ones(sensing_matrix.shape[1]), sensing_matrix))
xstar, rnorm = scipy.optimize.nnls(sensing_matrix, counts)
xstar = xstar / xstar.sum(0)
return xstar
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