A C++11 conformant compiler (currently tested with GCC>=4.7 and Clang>=3.4)
CMake. Sailfish uses the CMake build system to check, fetch and install
dependencies, and to compile and install Sailfish. CMake is available for all
major platforms (though Sailfish is currently unsupported on Windows.)
After downloading the Sailfish source distribution and unpacking it, change into the top-level directory:
> cd Sailfish
Then, create and out-of-source build directory and change into it:
> mkdir build
> cd build
Sailfish makes extensive use of Boost. We recommend installing the most
recent version (1.55) systemwide if possible. If Boost is not installed on your
system, the build process will fetch, compile and install it locally. However,
if you already have a recent version of Boost available on your system, it make
sense to tell the build system to use that.
If you have Boost installed you can tell CMake where to look for it. Likewise,
if you already have Intel’s Threading Building Blocks library installed, you can tell CMake
where it is as well. The flags for CMake are as follows:
-DFETCH_BOOST=TRUE – If you don’t have Boost installed (or have an older
version of it), you can provide the FETCH_BOOST flag instead of the
BOOST_ROOT variable, which will cause CMake to fetch and build Boost locally.
-DBOOST_ROOT=<boostdir> – Tells CMake where an existing installtion of Boost
resides, and looks for the appropritate version in <boostdir>. This is the
top-level directory where Boost is installed (e.g. /opt/local).
-DTBB_INSTALL_DIR=<tbbroot> – Tells CMake where an existing installation of
Intel’s TBB is installed (<tbbroot>), and looks for the apropriate headers
and libraries there. This is the top-level directory where TBB is installed
(e.g. /opt/local).
-DCMAKE_INSTALL_PREFIX=<install_dir> – <install_dir> is the directory to
which you wish Sailfish to be installed. If you don’t specify this option,
it will be installed locally in the top-level directory (i.e. the directory
directly above “build”).
Setting the appropriate flags, you can then run the CMake configure step as
follows:
> cmake [FLAGS] ..
The above command is the cmake configuration step, which should complain if
anything goes wrong. Next, you have to run the build step. Depending on what
libraries need to be fetched and installed, this could take a while
(specifically if the installation needs to install Boost). To start the build,
just run make.
> make
If the build is successful, the appropriate executables and libraries should be
created. There are two points to note about the build process. First, if the
build system is downloading and compiling boost, you may see a large number of
warnings during compilation; these are normal. Second, note that CMake has
colored output by default, and the steps which create or link libraries are
printed in red. This is the color chosen by CMake for linking messages, and
does not denote an error in the build process.
Finally, after everything is built, the libraries and executable can be
installed with:
> make install
To ensure that Sailfish has access to the appropriate libraries you should
ensure that the PATH variabile contains <install_dir>/bin, and that
LD_LIBRARY_PATH (or DYLD_FALLBACK_LIBRARY_PATH on OSX) contains
<install_dir>/lib.
After the paths are set, you can test the installation by running
> make test
This should run a simple test and tell you if it succeeded or not.
Sailfish is a tool for transcript quantification from RNA-seq data. It
requires a set of target transcripts (either from a reference or de-novo
assembly) to quantify. All you need to run sailfish is a fasta file containing
your reference transcripts and a (set of) fasta/fastq file(s) containing your
reads. Sailfish runs in two phases; indexing and quantification. The indexing
step is independent of the reads, and only needs to be run once for a particular
set of reference transcripts and choice of k (the k-mer size). The
quantification step, obviously, is specific to the set of RNA-seq reads and is
thus run more frequently.
To generate the sailfish index for your reference set of transcripts, you
should run the following command:
> sailfish index -t <ref_transcripts> -o <out_dir> -k <kmer_len>
This will build a sailfish index using k-mers of length <kmer_len> for the
reference transcripts provided in the file <ref_transcripts> and place the
index under the directory <out_dir>. There are additional options that can
be passed to the sailfish indexer (e.g. the number of threads to use). These
can be seen by executing the command sailfishindex-h.
Note that, as of v0.7.0, the meaning of the -k parameter has changed slightly.
Rather than the k-mer size on which Sailfish will quantify abundances, it becomes
the minimum match size that will be considered in the quasi-mapping
procedure during quantification. For sufficiently long (e.g. 75bp or greater)
reads, the default should be acceptable. If you have substantially shorter
reads, you may want to consider a smaller -k.
Note
values of k
The k value used to build the Sailfish index must be an odd number. Using an
even value for k will raise an error and the full index will not be built.
Now that you have generated the sailfish index (say that it’s the directory
<index_dir> — this corresponds to the <out_dir> argument provided in the
previous step), you can quantify the transcript expression for a given set of
reads. To perform the quantification, you run a command like the following:
Where <index_dir> is, as described above, the location of the sailfish
index, <libtype> is a string describing the format of the fragment (read)
library (see Fragment Library Types), <unmated> is a list of files
containing unmated reads, <mates{1,2}> are lists of files containg,
respectively, the first and second mates of paired-end reads. Finally,
<quant_dir> is the directory where the output should be written. Just like the
indexing step, additional options are available, and can be viewed by running
sailfishquant-h.
When the quantification step is finished, the directory <quant_dir> will
contain a file named “quant.sf” (and, if bias correction is enabled, an
additional file names “quant_bias_corrected.sf”). This file contains the
result of the Sailfish quantification step. This file contains a number of
columns (which are listed in the last of the header lines beginning with ‘#’).
Specifically, the columns are (1) Transcript ID, (2) Transcript Length, (3)
Transcripts per Million (TPM) and (6) Estimated number of reads (an estimate
of the number of reads drawn from this transcript given the transcript’s
relative abundance and length). The first two columns are self-explanatory,
the next four are measures of transcript abundance and the final is a commonly
used input for differential expression tools. The Transcripts per Million
quantification number is computed as described in [1], and is meant as an
estimate of the number of transcripts, per million observed transcripts,
originating from each isoform. Its benefit over the F/RPKM measure is that it
is independent of the mean expressed transcript length (i.e. if the mean
expressed transcript length varies between samples, for example, this alone can
affect differential analysis based on the K/RPKM.).
Sailfish exposes a number of useful optional command-line parameters to the user.
The particularly important ones are explained here, but you can always run
sailfishquant-h to see them all.
The number of threads that will be used for quasi-mapping, quantification, and
bootstrapping / posterior sampling (if enabled). Sailfish is designed to work
well with many threads, so, if you have a sufficient number of processors, larger
values here can speed up the run substantially.
Use the variational Bayesian EM algorithm rather than the “standard” EM algorithm
to optimize abundance estimates. The details of the VBEM algorithm can be found
in [2], and the details of the variant over fragment equivalence classes that
we use can be found in [3]. While both the standard EM and the VBEM produce
accurate abundance estimates, those produced by the VBEM seem, generally, to be
a bit more accurate. Further, the VBEM tends to converge after fewer iterations,
so it may result in a shorter runtime; especially if you are computing many
bootstrap samples.
Sailfish has the ability to optionally compute bootstrapped abundance estimates.
This is done by resampling (with replacement) from the counts assigned to
the fragment equivalence classes, and then re-running the optimization procedure,
either the EM or VBEM, for each such sample. The values of these different
bootstraps allows us to assess technical variance in the main abundance estimates
we produce. Such estimates can be useful for downstream (e.g. differential
expression) tools that can make use of such uncertainty estimates. This option
takes a positive integer that dictates the number of bootstrap samples to compute.
The more samples computed, the better the estimates of varaiance, but the
more computation (and time) required.
Just as with the bootstrap procedure above, this option produces samples that allow
us to estimate the variance in abundance estimates. However, in this case the
samples are generated using posterior Gibbs sampling over the fragment equivalence
classes rather than bootstrapping. We are currently analyzing these different approaches
to assess the potential trade-offs in time / accuracy. The --numBootstraps and
--numGibbsSamples options are mutually exclusive (i.e. in a given run, you must
set at most one of these options to a positive integer.)
Nariai, Naoki, et al. “TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.”
Bioinformatics (2013): btt381.
Rob Patro, Geet Duggal & Carl Kingsford “Accurate, fast, and model-aware transcript expression quantification with Salmon”
bioRxiv doi: http://dx.doi.org/10.1101/021592
There are numerous library preparation protocols for RNA-seq that result in
sequencing reads with different characteristics. For example, reads can be
single end (only one side of a fragment is recorded as a read) or paired-end
(reads are generated from both ends of a fragment). Further, the sequencing
reads themselves may be unstraned or strand-specific. Finally, paired-end
protocols will have a specified relative orientation. To characterize the
various different typs of sequencing libraries, we’ve created a miniature
“language” that allows for the succinct description of the many different types
of possible fragment libraries. For paired-end reads, the possible
orientations, along with a graphical description of what they mean, are
illustrated below:
The library type string consists of three parts: the relative orientation of
the reads, the strandedness of the library, and the directionality of the
reads.
The first part of the library string (relative orientation) is only provided if
the library is paired-end. The possible options are:
I=inwardO=outwardM=matching
The second part of the read library string specifies whether the protocol is
stranded or unstranded; the options are:
S=strandedU=unstranded
If the protocol is unstranded, then we’re done. The final part of the library
string specifies the strand from which the read originates in a strand-specific
protocol — it is only provided if the library is stranded (i.e. if the
library format string is of the form S). The possible values are:
F = read 1 (or single-end read) comes from the forward strand
R = read 1 (or single-end read) comes from the reverse strand
So, for example, if you wanted to specify a fragment library of strand-specific
paired-end reads, oriented toward each other, where read 1 comes from the
forward strand and read 2 comes from the reverse strand, you would specify -lISF on the command line. This designates that the library being processed has
the type “ISF” meaning, Inward (the relative orientation), Stranted
(the protocol is strand-specific), Forward (read 1 comes from the forward
strand).
The single end library strings are a bit simpler than their pair-end counter
parts, since there is no relative orientation of which to speak. Thus, the
only possible library format types for single-end reads are U (for
unstranded), SF (for strand-specific reads coming from the forward strand)
and SR (for strand-specific reads coming from the reverse strand).
A few more examples of some library format strings and their interpretations are:
IU (an unstranded paired-end library where the reads face each other)
SF (a stranded single-end protocol where the reads come from the forward strand)
OSR (a stranded paired-end protocol where the reads face away from each other,
read1 comes from reverse strand and read2 comes from the forward strand)
Note
Correspondence to TopHat library types
The popular TopHat RNA-seq
read aligner has a different convention for specifying the format of the library.
Below is a table that provides the corresponding sailfish/salmon library format
string for each of the potential TopHat library types:
TopHat
Salmon (and Sailfish)
Paired-end
Single-end
-fr-unstranded
-lIU
-lU
-fr-firststrand
-lISR
-lSR
-fr-secondstrand
-lISF
-lSF
The remaining salmon library format strings are not directly expressible in terms
of the TopHat library types, and so there is no direct mapping for them.
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// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
// Underscore is freely distributable under the MIT license.
// Portions of Underscore are inspired or borrowed from Prototype,
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// For all details and documentation:
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// Return the number of elements in an object.
_.size = function(obj) {
return _.toArray(obj).length;
};
// Array Functions
// ---------------
// Get the first element of an array. Passing **n** will return the first N
// values in the array. Aliased as `head`. The **guard** check allows it to work
// with `_.map`.
_.first = _.head = function(array, n, guard) {
return (n != null) && !guard ? slice.call(array, 0, n) : array[0];
};
// Returns everything but the last entry of the array. Especcialy useful on
// the arguments object. Passing **n** will return all the values in
// the array, excluding the last N. The **guard** check allows it to work with
// `_.map`.
_.initial = function(array, n, guard) {
return slice.call(array, 0, array.length - ((n == null) || guard ? 1 : n));
};
// Get the last element of an array. Passing **n** will return the last N
// values in the array. The **guard** check allows it to work with `_.map`.
_.last = function(array, n, guard) {
if ((n != null) && !guard) {
return slice.call(array, Math.max(array.length - n, 0));
} else {
return array[array.length - 1];
}
};
// Returns everything but the first entry of the array. Aliased as `tail`.
// Especially useful on the arguments object. Passing an **index** will return
// the rest of the values in the array from that index onward. The **guard**
// check allows it to work with `_.map`.
_.rest = _.tail = function(array, index, guard) {
return slice.call(array, (index == null) || guard ? 1 : index);
};
// Trim out all falsy values from an array.
_.compact = function(array) {
return _.filter(array, function(value){ return !!value; });
};
// Return a completely flattened version of an array.
_.flatten = function(array, shallow) {
return _.reduce(array, function(memo, value) {
if (_.isArray(value)) return memo.concat(shallow ? value : _.flatten(value));
memo[memo.length] = value;
return memo;
}, []);
};
// Return a version of the array that does not contain the specified value(s).
_.without = function(array) {
return _.difference(array, slice.call(arguments, 1));
};
// Produce a duplicate-free version of the array. If the array has already
// been sorted, you have the option of using a faster algorithm.
// Aliased as `unique`.
_.uniq = _.unique = function(array, isSorted, iterator) {
var initial = iterator ? _.map(array, iterator) : array;
var result = [];
_.reduce(initial, function(memo, el, i) {
if (0 == i || (isSorted === true ? _.last(memo) != el : !_.include(memo, el))) {
memo[memo.length] = el;
result[result.length] = array[i];
}
return memo;
}, []);
return result;
};
// Produce an array that contains the union: each distinct element from all of
// the passed-in arrays.
_.union = function() {
return _.uniq(_.flatten(arguments, true));
};
// Produce an array that contains every item shared between all the
// passed-in arrays. (Aliased as "intersect" for back-compat.)
_.intersection = _.intersect = function(array) {
var rest = slice.call(arguments, 1);
return _.filter(_.uniq(array), function(item) {
return _.every(rest, function(other) {
return _.indexOf(other, item) >= 0;
});
});
};
// Take the difference between one array and a number of other arrays.
// Only the elements present in just the first array will remain.
_.difference = function(array) {
var rest = _.flatten(slice.call(arguments, 1));
return _.filter(array, function(value){ return !_.include(rest, value); });
};
// Zip together multiple lists into a single array -- elements that share
// an index go together.
_.zip = function() {
var args = slice.call(arguments);
var length = _.max(_.pluck(args, 'length'));
var results = new Array(length);
for (var i = 0; i < length; i++) results[i] = _.pluck(args, "" + i);
return results;
};
// If the browser doesn't supply us with indexOf (I'm looking at you, **MSIE**),
// we need this function. Return the position of the first occurrence of an
// item in an array, or -1 if the item is not included in the array.
// Delegates to **ECMAScript 5**'s native `indexOf` if available.
// If the array is large and already in sort order, pass `true`
// for **isSorted** to use binary search.
_.indexOf = function(array, item, isSorted) {
if (array == null) return -1;
var i, l;
if (isSorted) {
i = _.sortedIndex(array, item);
return array[i] === item ? i : -1;
}
if (nativeIndexOf && array.indexOf === nativeIndexOf) return array.indexOf(item);
for (i = 0, l = array.length; i < l; i++) if (i in array && array[i] === item) return i;
return -1;
};
// Delegates to **ECMAScript 5**'s native `lastIndexOf` if available.
_.lastIndexOf = function(array, item) {
if (array == null) return -1;
if (nativeLastIndexOf && array.lastIndexOf === nativeLastIndexOf) return array.lastIndexOf(item);
var i = array.length;
while (i--) if (i in array && array[i] === item) return i;
return -1;
};
// Generate an integer Array containing an arithmetic progression. A port of
// the native Python `range()` function. See
// [the Python documentation](http://docs.python.org/library/functions.html#range).
_.range = function(start, stop, step) {
if (arguments.length <= 1) {
stop = start || 0;
start = 0;
}
step = arguments[2] || 1;
var len = Math.max(Math.ceil((stop - start) / step), 0);
var idx = 0;
var range = new Array(len);
while(idx < len) {
range[idx++] = start;
start += step;
}
return range;
};
// Function (ahem) Functions
// ------------------
// Reusable constructor function for prototype setting.
var ctor = function(){};
// Create a function bound to a given object (assigning `this`, and arguments,
// optionally). Binding with arguments is also known as `curry`.
// Delegates to **ECMAScript 5**'s native `Function.bind` if available.
// We check for `func.bind` first, to fail fast when `func` is undefined.
_.bind = function bind(func, context) {
var bound, args;
if (func.bind === nativeBind && nativeBind) return nativeBind.apply(func, slice.call(arguments, 1));
if (!_.isFunction(func)) throw new TypeError;
args = slice.call(arguments, 2);
return bound = function() {
if (!(this instanceof bound)) return func.apply(context, args.concat(slice.call(arguments)));
ctor.prototype = func.prototype;
var self = new ctor;
var result = func.apply(self, args.concat(slice.call(arguments)));
if (Object(result) === result) return result;
return self;
};
};
// Bind all of an object's methods to that object. Useful for ensuring that
// all callbacks defined on an object belong to it.
_.bindAll = function(obj) {
var funcs = slice.call(arguments, 1);
if (funcs.length == 0) funcs = _.functions(obj);
each(funcs, function(f) { obj[f] = _.bind(obj[f], obj); });
return obj;
};
// Memoize an expensive function by storing its results.
_.memoize = function(func, hasher) {
var memo = {};
hasher || (hasher = _.identity);
return function() {
var key = hasher.apply(this, arguments);
return _.has(memo, key) ? memo[key] : (memo[key] = func.apply(this, arguments));
};
};
// Delays a function for the given number of milliseconds, and then calls
// it with the arguments supplied.
_.delay = function(func, wait) {
var args = slice.call(arguments, 2);
return setTimeout(function(){ return func.apply(func, args); }, wait);
};
// Defers a function, scheduling it to run after the current call stack has
// cleared.
_.defer = function(func) {
return _.delay.apply(_, [func, 1].concat(slice.call(arguments, 1)));
};
// Returns a function, that, when invoked, will only be triggered at most once
// during a given window of time.
_.throttle = function(func, wait) {
var context, args, timeout, throttling, more;
var whenDone = _.debounce(function(){ more = throttling = false; }, wait);
return function() {
context = this; args = arguments;
var later = function() {
timeout = null;
if (more) func.apply(context, args);
whenDone();
};
if (!timeout) timeout = setTimeout(later, wait);
if (throttling) {
more = true;
} else {
func.apply(context, args);
}
whenDone();
throttling = true;
};
};
// Returns a function, that, as long as it continues to be invoked, will not
// be triggered. The function will be called after it stops being called for
// N milliseconds.
_.debounce = function(func, wait) {
var timeout;
return function() {
var context = this, args = arguments;
var later = function() {
timeout = null;
func.apply(context, args);
};
clearTimeout(timeout);
timeout = setTimeout(later, wait);
};
};
// Returns a function that will be executed at most one time, no matter how
// often you call it. Useful for lazy initialization.
_.once = function(func) {
var ran = false, memo;
return function() {
if (ran) return memo;
ran = true;
return memo = func.apply(this, arguments);
};
};
// Returns the first function passed as an argument to the second,
// allowing you to adjust arguments, run code before and after, and
// conditionally execute the original function.
_.wrap = function(func, wrapper) {
return function() {
var args = [func].concat(slice.call(arguments, 0));
return wrapper.apply(this, args);
};
};
// Returns a function that is the composition of a list of functions, each
// consuming the return value of the function that follows.
_.compose = function() {
var funcs = arguments;
return function() {
var args = arguments;
for (var i = funcs.length - 1; i >= 0; i--) {
args = [funcs[i].apply(this, args)];
}
return args[0];
};
};
// Returns a function that will only be executed after being called N times.
_.after = function(times, func) {
if (times <= 0) return func();
return function() {
if (--times < 1) { return func.apply(this, arguments); }
};
};
// Object Functions
// ----------------
// Retrieve the names of an object's properties.
// Delegates to **ECMAScript 5**'s native `Object.keys`
_.keys = nativeKeys || function(obj) {
if (obj !== Object(obj)) throw new TypeError('Invalid object');
var keys = [];
for (var key in obj) if (_.has(obj, key)) keys[keys.length] = key;
return keys;
};
// Retrieve the values of an object's properties.
_.values = function(obj) {
return _.map(obj, _.identity);
};
// Return a sorted list of the function names available on the object.
// Aliased as `methods`
_.functions = _.methods = function(obj) {
var names = [];
for (var key in obj) {
if (_.isFunction(obj[key])) names.push(key);
}
return names.sort();
};
// Extend a given object with all the properties in passed-in object(s).
_.extend = function(obj) {
each(slice.call(arguments, 1), function(source) {
for (var prop in source) {
obj[prop] = source[prop];
}
});
return obj;
};
// Fill in a given object with default properties.
_.defaults = function(obj) {
each(slice.call(arguments, 1), function(source) {
for (var prop in source) {
if (obj[prop] == null) obj[prop] = source[prop];
}
});
return obj;
};
// Create a (shallow-cloned) duplicate of an object.
_.clone = function(obj) {
if (!_.isObject(obj)) return obj;
return _.isArray(obj) ? obj.slice() : _.extend({}, obj);
};
// Invokes interceptor with the obj, and then returns obj.
// The primary purpose of this method is to "tap into" a method chain, in
// order to perform operations on intermediate results within the chain.
_.tap = function(obj, interceptor) {
interceptor(obj);
return obj;
};
// Internal recursive comparison function.
function eq(a, b, stack) {
// Identical objects are equal. `0 === -0`, but they aren't identical.
// See the Harmony `egal` proposal: http://wiki.ecmascript.org/doku.php?id=harmony:egal.
if (a === b) return a !== 0 || 1 / a == 1 / b;
// A strict comparison is necessary because `null == undefined`.
if (a == null || b == null) return a === b;
// Unwrap any wrapped objects.
if (a._chain) a = a._wrapped;
if (b._chain) b = b._wrapped;
// Invoke a custom `isEqual` method if one is provided.
if (a.isEqual && _.isFunction(a.isEqual)) return a.isEqual(b);
if (b.isEqual && _.isFunction(b.isEqual)) return b.isEqual(a);
// Compare `[[Class]]` names.
var className = toString.call(a);
if (className != toString.call(b)) return false;
switch (className) {
// Strings, numbers, dates, and booleans are compared by value.
case '[object String]':
// Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is
// equivalent to `new String("5")`.
return a == String(b);
case '[object Number]':
// `NaN`s are equivalent, but non-reflexive. An `egal` comparison is performed for
// other numeric values.
return a != +a ? b != +b : (a == 0 ? 1 / a == 1 / b : a == +b);
case '[object Date]':
case '[object Boolean]':
// Coerce dates and booleans to numeric primitive values. Dates are compared by their
// millisecond representations. Note that invalid dates with millisecond representations
// of `NaN` are not equivalent.
return +a == +b;
// RegExps are compared by their source patterns and flags.
case '[object RegExp]':
return a.source == b.source &&
a.global == b.global &&
a.multiline == b.multiline &&
a.ignoreCase == b.ignoreCase;
}
if (typeof a != 'object' || typeof b != 'object') return false;
// Assume equality for cyclic structures. The algorithm for detecting cyclic
// structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`.
var length = stack.length;
while (length--) {
// Linear search. Performance is inversely proportional to the number of
// unique nested structures.
if (stack[length] == a) return true;
}
// Add the first object to the stack of traversed objects.
stack.push(a);
var size = 0, result = true;
// Recursively compare objects and arrays.
if (className == '[object Array]') {
// Compare array lengths to determine if a deep comparison is necessary.
size = a.length;
result = size == b.length;
if (result) {
// Deep compare the contents, ignoring non-numeric properties.
while (size--) {
// Ensure commutative equality for sparse arrays.
if (!(result = size in a == size in b && eq(a[size], b[size], stack))) break;
}
}
} else {
// Objects with different constructors are not equivalent.
if ('constructor' in a != 'constructor' in b || a.constructor != b.constructor) return false;
// Deep compare objects.
for (var key in a) {
if (_.has(a, key)) {
// Count the expected number of properties.
size++;
// Deep compare each member.
if (!(result = _.has(b, key) && eq(a[key], b[key], stack))) break;
}
}
// Ensure that both objects contain the same number of properties.
if (result) {
for (key in b) {
if (_.has(b, key) && !(size--)) break;
}
result = !size;
}
}
// Remove the first object from the stack of traversed objects.
stack.pop();
return result;
}
// Perform a deep comparison to check if two objects are equal.
_.isEqual = function(a, b) {
return eq(a, b, []);
};
// Is a given array, string, or object empty?
// An "empty" object has no enumerable own-properties.
_.isEmpty = function(obj) {
if (_.isArray(obj) || _.isString(obj)) return obj.length === 0;
for (var key in obj) if (_.has(obj, key)) return false;
return true;
};
// Is a given value a DOM element?
_.isElement = function(obj) {
return !!(obj && obj.nodeType == 1);
};
// Is a given value an array?
// Delegates to ECMA5's native Array.isArray
_.isArray = nativeIsArray || function(obj) {
return toString.call(obj) == '[object Array]';
};
// Is a given variable an object?
_.isObject = function(obj) {
return obj === Object(obj);
};
// Is a given variable an arguments object?
_.isArguments = function(obj) {
return toString.call(obj) == '[object Arguments]';
};
if (!_.isArguments(arguments)) {
_.isArguments = function(obj) {
return !!(obj && _.has(obj, 'callee'));
};
}
// Is a given value a function?
_.isFunction = function(obj) {
return toString.call(obj) == '[object Function]';
};
// Is a given value a string?
_.isString = function(obj) {
return toString.call(obj) == '[object String]';
};
// Is a given value a number?
_.isNumber = function(obj) {
return toString.call(obj) == '[object Number]';
};
// Is the given value `NaN`?
_.isNaN = function(obj) {
// `NaN` is the only value for which `===` is not reflexive.
return obj !== obj;
};
// Is a given value a boolean?
_.isBoolean = function(obj) {
return obj === true || obj === false || toString.call(obj) == '[object Boolean]';
};
// Is a given value a date?
_.isDate = function(obj) {
return toString.call(obj) == '[object Date]';
};
// Is the given value a regular expression?
_.isRegExp = function(obj) {
return toString.call(obj) == '[object RegExp]';
};
// Is a given value equal to null?
_.isNull = function(obj) {
return obj === null;
};
// Is a given variable undefined?
_.isUndefined = function(obj) {
return obj === void 0;
};
// Has own property?
_.has = function(obj, key) {
return hasOwnProperty.call(obj, key);
};
// Utility Functions
// -----------------
// Run Underscore.js in *noConflict* mode, returning the `_` variable to its
// previous owner. Returns a reference to the Underscore object.
_.noConflict = function() {
root._ = previousUnderscore;
return this;
};
// Keep the identity function around for default iterators.
_.identity = function(value) {
return value;
};
// Run a function **n** times.
_.times = function (n, iterator, context) {
for (var i = 0; i < n; i++) iterator.call(context, i);
};
// Escape a string for HTML interpolation.
_.escape = function(string) {
return (''+string).replace(/&/g, '&').replace(//g, '>').replace(/"/g, '"').replace(/'/g, ''').replace(/\//g,'/');
};
// Add your own custom functions to the Underscore object, ensuring that
// they're correctly added to the OOP wrapper as well.
_.mixin = function(obj) {
each(_.functions(obj), function(name){
addToWrapper(name, _[name] = obj[name]);
});
};
// Generate a unique integer id (unique within the entire client session).
// Useful for temporary DOM ids.
var idCounter = 0;
_.uniqueId = function(prefix) {
var id = idCounter++;
return prefix ? prefix + id : id;
};
// By default, Underscore uses ERB-style template delimiters, change the
// following template settings to use alternative delimiters.
_.templateSettings = {
evaluate : /<%([\s\S]+?)%>/g,
interpolate : /<%=([\s\S]+?)%>/g,
escape : /<%-([\s\S]+?)%>/g
};
// When customizing `templateSettings`, if you don't want to define an
// interpolation, evaluation or escaping regex, we need one that is
// guaranteed not to match.
var noMatch = /.^/;
// Within an interpolation, evaluation, or escaping, remove HTML escaping
// that had been previously added.
var unescape = function(code) {
return code.replace(/\\\\/g, '\\').replace(/\\'/g, "'");
};
// JavaScript micro-templating, similar to John Resig's implementation.
// Underscore templating handles arbitrary delimiters, preserves whitespace,
// and correctly escapes quotes within interpolated code.
_.template = function(str, data) {
var c = _.templateSettings;
var tmpl = 'var __p=[],print=function(){__p.push.apply(__p,arguments);};' +
'with(obj||{}){__p.push(\'' +
str.replace(/\\/g, '\\\\')
.replace(/'/g, "\\'")
.replace(c.escape || noMatch, function(match, code) {
return "',_.escape(" + unescape(code) + "),'";
})
.replace(c.interpolate || noMatch, function(match, code) {
return "'," + unescape(code) + ",'";
})
.replace(c.evaluate || noMatch, function(match, code) {
return "');" + unescape(code).replace(/[\r\n\t]/g, ' ') + ";__p.push('";
})
.replace(/\r/g, '\\r')
.replace(/\n/g, '\\n')
.replace(/\t/g, '\\t')
+ "');}return __p.join('');";
var func = new Function('obj', '_', tmpl);
if (data) return func(data, _);
return function(data) {
return func.call(this, data, _);
};
};
// Add a "chain" function, which will delegate to the wrapper.
_.chain = function(obj) {
return _(obj).chain();
};
// The OOP Wrapper
// ---------------
// If Underscore is called as a function, it returns a wrapped object that
// can be used OO-style. This wrapper holds altered versions of all the
// underscore functions. Wrapped objects may be chained.
var wrapper = function(obj) { this._wrapped = obj; };
// Expose `wrapper.prototype` as `_.prototype`
_.prototype = wrapper.prototype;
// Helper function to continue chaining intermediate results.
var result = function(obj, chain) {
return chain ? _(obj).chain() : obj;
};
// A method to easily add functions to the OOP wrapper.
var addToWrapper = function(name, func) {
wrapper.prototype[name] = function() {
var args = slice.call(arguments);
unshift.call(args, this._wrapped);
return result(func.apply(_, args), this._chain);
};
};
// Add all of the Underscore functions to the wrapper object.
_.mixin(_);
// Add all mutator Array functions to the wrapper.
each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) {
var method = ArrayProto[name];
wrapper.prototype[name] = function() {
var wrapped = this._wrapped;
method.apply(wrapped, arguments);
var length = wrapped.length;
if ((name == 'shift' || name == 'splice') && length === 0) delete wrapped[0];
return result(wrapped, this._chain);
};
});
// Add all accessor Array functions to the wrapper.
each(['concat', 'join', 'slice'], function(name) {
var method = ArrayProto[name];
wrapper.prototype[name] = function() {
return result(method.apply(this._wrapped, arguments), this._chain);
};
});
// Start chaining a wrapped Underscore object.
wrapper.prototype.chain = function() {
this._chain = true;
return this;
};
// Extracts the result from a wrapped and chained object.
wrapper.prototype.value = function() {
return this._wrapped;
};
}).call(this);
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