Free comparisons software for linux

Bio::SAGE::Comparison module compares data from serial analysis of gene expression (SAGE) libraries.

SYNOPSIS

use Bio::SAGE::Comparison;
$sage = Bio::SAGE::Comparison->new();

This module provides several tools for comparing data generated from serial analysis of gene expression (SAGE) libraries.

BACKGROUND

Serial analysis of gene expression (SAGE) is a molecular technique for generating a near-global snapshot of a cell population’s transcriptome. Briefly, the technique extracts short sequences at defined positions of transcribed mRNA. These short sequences are then paired to form ditags. The ditags are concatamerized to form long sequences that are then cloned. The cloned DNA is then sequenced. Bioinformatic techniques are then employed to determine the original short tag sequences, and to derive their progenitor mRNA. The number of times a particular tag is observed can be used to quantitate the amount of a particular transcript. The original technique was described by Velculescu et al. (1995) and utilized an ~14bp sequence tag. A modified protocol was introduced by Saha et al. (2002) that produced ~21bp tags.

PURPOSE

This module facilitates the comparison of SAGE libraries. Specifically:

1. Calculations for determining the statistical
significance of expression differences.
2. Dynamically convert longer-tag libraries to
a shorter type for comparison (e.g. comparing
a LongSAGE vs. a regular SAGE library).

Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module.

Statistical significance in library comparisons is calculated using the method described by Audic and Claverie (1997). Code was generated by directly porting the authors original C source.

Komparator is an application that searches and synchronizes two directories. Komparator project discovers duplicate, newer or missing files and empty folders.
It works on local and some network / kioslave protocol folders (like smb:/ and media:/).
It is still in an early stage; please try on test directories first.
Main features:
- ftp et alii supported (might still be buggy!).
- Keyboard shortcuts (popup menus didnt work, unfortunately) fixed.
- Drag & drop missing / newer files from left to right side & vice versa.
- Special characters in URLs fixed.
- Cancel button isnt locked any more if md5-summing / binary comparing remote files.
- Status bar including progress of kompare and about / help button.
- Source code cleanups.
- GUI cleanups.
- Resize list view columns to original width.
- Binary comparison wont store the complete file in RAM any more.
- First documentation attempt.
Enhancements:
- Filters to display only specific files
- Regex that the file name may not contain
- In-/Exclude hidden items
- Some bug fixes

Kernel Configuration Comparison (kccmp) provides a GUI for comparing two Linux kernel ".config" files.
It shows configuration variables with different values in a tabular format. It also shows configuration variables found in only one of the input configuration files.
Building:
kccmp by default requires Qt 3.x. However, by changing one line in kccmp.pro you can build against Qt 4.x. Note that the Qt 4.x build requilres libboost_regex as well.
The standard build is as easy as:
example:
% qmake
% make
Usage
% kccmp /path/to/first/.config path/to/second/.config
example:
% kccmp /usr/src/linux/.config /usr/src/linux/.config.old
Enhancements:
- This release was ported to Qt 3.x.
- The requirement for libboost_regex was removed.
- Building with either Qt 4.x or Qt 3.x is now supported.

Schema-compare is a script that will compares two database schema and show the differences side-by-side.
Schema-compare can also generate SQL statements that will alter the old database to match the schema of the new database.
The comparisons are correct, but the SQL statements at the bottom are not quite right, they are close to what is necessary, but probably not exactly right.
To install simply ungzip/untar the file wherever you want to put it in your web folder and then edit the include/config.inc.php file with the information needed to connect to the two databases you want to compare. Both databases need to be on the same database server and use the same username and password to connect to them.
Enhancements:
- This is the first release of schema-compare. It compares the database schema just fine, but the sql alter statements it creates could use some work.

SYNOPSIS

use Array::Compare;

my $comp1 = Array::Compare->new;
$comp->Sep(|);
$comp->Skip({3 => 1, 4 => 1});
$comp->WhiteSpace(0);
$comp->Case(1);

my $comp2 = Array::Compare->new(Sep => |,
WhiteSpace => 0,
Case => 1,
Skip => {3 => 1, 4 => 1});

my @arr1 = 0 .. 10;
my @arr2 = 0 .. 10;

$comp1->compare(@arr1, @arr2);
$comp2->compare(@arr1, @arr2);

If you have two arrays and you want to know if they are the same or different, then Array::Compare will be useful to you.
All comparisons are carried out via a comparator object. In the simplest usage, you can create and use a comparator object like this:

my @arr1 = 0 .. 10;
my @arr2 = 0 .. 10;

my $comp = Array::Compare->new;

if ($comp->compare(@arr1, @arr2)) {
print "Arrays are the samen";
} else {
print "Arrays are differentn";
}

Notice that you pass references to the two arrays to the comparison method.

Internally the comparator compares the two arrays by using join to turn both arrays into strings and comparing the strings using eq. In the joined strings, the elements of the original arrays are separated with the ^G character. This can cause problems if your array data contains ^G characters as it is possible that two different arrays can be converted to the same string.

To avoid this, it is possible to override the default separator character, either by passing and alternative to the new function

my $comp = Array::Compare->new(Sep => |);

or by changing the seperator for an existing comparator object

$comp->Sep(|);

In general you should choose a separator character that wont appear in your data.

You can also control whether or not whitespace within the elements of the arrays should be considered significant when making the comparison. The default is that all whitespace is significant. The alternative is for all consecutive white space characters to be converted to a single space for the pruposes of the comparison. Again, this can be turned on when creating a comparator object:

my $comp = Array::Compare->new(WhiteSpace => 0);

or by altering an existing object:

$comp->WhiteSpace(0);

You can also control whether or not the case of the data is significant in the comparison. The default is that the case of data is taken into account. This can be changed in the standard ways when creating a new comparator object:

my $comp = Array::Compare->new(Case => 0);

or by altering an existing object:

$comp->Case(0);

In addition to the simple comparison described above (which returns true if the arrays are the same and false if theyre different) there is also a full comparison which returns a list containing the indexes of elements which differ between the two arrays. If the arrays are the same it returns an empty list. In scalar context the full comparison returns the length of this list (i.e. the number of elements that differ). You can access the full comparision in two ways. Firstly, there is a DefFull attribute. If this is true then a full comparison if carried out whenever the compare method is called.

my $comp = Array::Compare->new(DefFull => 1);
$comp->compare(@arr1, @arr2); # Full comparison

$comp->DefFull(0);
$comp->compare(@arr1, @arr2); # Simple comparison

$comp->DefFull(1);
$comp->compare(@arr1, @arr2); # Full comparison again

Secondly, you can access the full comparison method directly

$comp->full_compare(@arr1, @arr2);

For symmetry, there is also a direct method to use to call the simple comparison.

$comp->simple_compare(@arr1, @arr2);

The final complication is the ability to skip elements in the comparison. If you know that two arrays will always differ in a particular element but want to compare the arrays ignoring this element, you can do it with Array::Compare without taking array slices. To do this, a comparator object has an optional attribute called Skip which is a reference to a hash. The keys in this hash are the indexes of the array elements and the values should be any true value for elements that should be skipped.

For example, if you want to compare two arrays, ignoring the values in elements two and four, you can do something like this:

my %skip = (2 => 1, 4 => 1);
my @a = (0, 1, 2, 3, 4, 5);
my @b = (0, 1, X, 3, X, 5);

my $comp = Array::Compare->new(Skip => %skip);

$comp->compare(@a, @b);

This should return true, as we are explicitly ignoring the columns which differ.

Of course, having created a comparator object with no skip hash, it is possible to add one later:

$comp->Skip({1 => 1, 2 => 1});

or:

my %skip = (1 => 1, 2 => 2);
$comp->Skip(%skip);

To reset the comparator so that no longer skips elements, set the skip hash to an empty hash.

$comp->Skip({});

You can also check to see if one array is a permutation of another, i.e. they contain the same elements but in a different order.

if ($comp->perm(@a, @b) {
print "Arrays are permsn";
else {
print "Nope. Arrays are completely differentn";
}

In this case the values of WhiteSpace and Case are still used, but Skip is ignored for, hopefully, obvious reasons.

Struct::Compare is a recursive diff for perl structures.

SYNOPSIS

use Struct::Compare;
my $is_different = compare($ref1, $ref2);

Compares two values of any type and structure and returns true if they are the same. It does a deep comparison of the structures, so a hash of a hash of a whatever will be compared correctly.

This is especially useful for writing unit tests for your modules!

PUBLIC FUNCTIONS

$bool = compare($var1, $var2)

Recursively compares $var1 to $var2, returning false if either structure is different than the other at any point. If both are undefined, it returns true as well, because that is considered equal.

Benchmark::Forking is a Perl module to run benchmarks in separate processes.

SYNOPSIS

use Benchmark::Forking qw( timethis timethese cmpthese );

timethis ($count, "code");

timethese($count, {
Name1 => sub { ...code1... },
Name2 => sub { ...code2... },
});

cmpthese($count, {
Name1 => sub { ...code1... },
Name2 => sub { ...code2... },
});

Benchmark::Forking->enabled(0); # Stop using forking feature
...
Benchmark::Forking->enabled(1); # Begin using forking again

The Benchmark::Forking module changes the behavior of the standard Benchmark module, running each piece of code to be timed in a separate forked process. Because each child exits after running its timing loop, the computations it performs cant propogate back to affect subsequent test cases.

This can make benchmark comparisons more accurate, because the separate test cases are mostly isolated from side-effects caused by the others. Benchmark scripts typically dont depend on those side-effects, so in most cases you can simply use or require this module at the top of your existing code without having to change anything else. (A few key exceptions are noted in "BUGS".)

Genezzo::Havok::SQLCompare is a Perl module with SQL comparison functions.
SYNOPSIS
HavokUse("Genezzo::Havok::SQLCompare")
FUNCTIONS
SQL functions
IN
WHERE value IN (list)
Returns TRUE if the value is present in the list, else FALSE. NOT IN is slightly different: returns NULL if any list item is NULL, return FALSE if the value matches any list item, else returns TRUE.
LIKE
WHERE value LIKE (pattern)
WHERE value LIKE (pattern, escape_char)
Returns TRUE if the value matches the pattern. In the pattern, a % (percent sign) matches zero or more characters, and an _ (underscore) matches exactly one character. These characters can be matched as literals if they are preceded by the optional escape character.
LIMITATIONS
- IN has list support, but no IN subquery support.
- LIKE has a "functional" syntax, instead of the standard LIKE pattern [ESCAPE escape_char].