wasade

#include <gsl/gsl_rng.h>
#include <math.h>
#include "subsample.h"

/* subsample_col
 *
 * desc: subsample an array of COO objects, of length size, to a sum of (n)
 *
 * inputs: COO* list - an array of COO objects
 *         COO* ss_result - store the subsampled result

wasade

#!/usr/bin/env python
from __future__ import with_statement
import os
import re
import shutil
import subprocess
import sys
import tempfile

wasade

#include <stdlib.h>
#include "symbol_table.h"

typedef struct STNode* stlink;
struct STNode {
    int index, d;
    stlink l, m, r; // left, middle, right
};

static stlink head;

wasade

wasade

wasade

# on github, go the your favorite repository, such as pyqi:
# https://github.com/bipy/pyqi
# click fork, this will create a copy of the forked repository (and branch, generally its master by default)

# on the command line, this will create a ./pyqi directory
$ git clone https://github.com/wasade/pyqi
$ cd pyqi

# update your remotes, this allows you to get updates from the master "origin" repository (bipy/pyqi in this case)
# we're going to call this upstream as it is upstream of your fork since other people merge to it

wasade

wasade

__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2013"
__credits__ = ["Daniel McDonald"]
__license__ = "BSD"
__version__ = "0.1"
__maintainer__ = "Daniel McDonald"
__email__ = "[email protected]"

usage = """%run cluster_utils.ipy

wasade

#!/usr/bin/env python27

from random import shuffle
from unittest import TestCase, main

__author__ = "Daniel McDonald"
__credits__ = ["Daniel McDonald"]
__license__ = "CC0 1.0, http://creativecommons.org/publicdomain/zero/1.0/"
__maintainer__ = "Daniel McDonald"
__url__ = "https://gist.github.com/wasade/7029970"

wasade

from qcli.interface.cli import CLOption, UsageExample, ParameterConversion

usage_examples = [
        UsageExample(ShortDesc="Abundance filtering (low coverage)",
                     LongDesc="Filter samples with fewer than 150 observations from the otu table.",
                     Ex="%prog -i otu_table.biom -o otu_table_no_low_coverage_samples.biom -n 150"),
        UsageExample(ShortDesc="Abundance filtering (high coverage)",
                     LongDesc="Filter samples with fewer than 150 observations from the otu table.",
                     Ex="%prog -i otu_table.biom -o otu_table_no_high_coverage_samples.biom -x 149")
        ]