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Bio::DB::Big XS bindings to libBigWig for access the UCSC/kent big formats

This library provides access to the BigWig and BigBed file formats designed by UCSC. However rather than use kent libraries this uses libBigWig from https://github.com/dpryan79/libBigWig as it provides an implementation that avoids exiting when errors happen. libBigWig provides access to BigWig summaries, values and intervals alongside providing access to BigBed entries.

andrewyatz@github 3 comments

Test::Contract Evaluate Test::More-like assertions in production code

1) Sometimes I feel like applying a series Test::More-like checks to user input, dynamically loaded plugin, object instance being passed etc. Unfortunately, Test::Builder makes it impossible without turning the whole application into a test script. Hence this OO interface.

2) Instead of using ok($condition, $message) as a foundation, this module uses a refute statement which is an inverted assertion. I.e. if everything is OK, we only need 1 bit of information; if something went wrong, we need more details. Think of Unix programs returning 0 on success and different error codes otherwise.

This way, extending the test arsenal becomes much simpler: a test function may know nothing about the test framework, it ONLY needs to try hard to find a discrepancy in its own arguments (aka pure function). A builder module is available that imports user's test subroutines into the main module.

3) Also supported: subcontracts to group complex checks, functional interface (Test::More compatible), checking that contract is fulfilled to exactly the given extent (useful for testing the test routines themselves).

dallaylaen@github 0 comments

C::Check, C::Critic, or C::Fuss static check of C programs

C compilers typically don't warn about daft mistakes like putting function arguments in the wrong order, or using the wrong size of a variable, or things like not checking the return value of malloc, etc. This module would check for typical errors in C programs like switch fallthroughs, use of equals instead of == in an if statement, insist on using braces with if statements, bad if statement indentation, like

if (x) 
      printf ("reached");
      printf ("reached even if x is not true, despite this indentation");

etc.

At the moment I have a script which does something like the above, wondering whether it would be worth working up into a module.

benkasminbullock@github 2 comments

Gram::Index Trigram index of files

I've been developing a C program which indexes files by making trigrams of the contents of files. It's working reasonably well now and I'm thinking of extending it to a Perl version which could be used to index files, database entries and other things.

benkasminbullock@github 0 comments

perltab command line utility for using perl code to manipulate data tables

perltab could be thought of as an extension to perl autosplit mode for handling tabular data. I developed while working with a bioinformatics dataset that quite a few features (columns) and many of them had missing values, which made the data inconvenient to directly handle with something like perl autosplit mode. With perl autosplit mode it is easy to output the nth column.

% perl -F'\t' -anE 'say $F[1]' heightWeight.tsv

perltab makes this slightly easier:

% perltab -e 'say $F[1]' heightWeight.tsv

But it also allows for using named columns (and allows for abbreviation)

% perltab -e 'say F(hei)' heightWeight.tsv

This is convenient, but when numerical computation and missing values come to play perltab is particularly helpful.

For example the minimum value of a column can be output in this way:

% perltab -d 'bemin $m, F(hei)' -z 'say $m'

or, as long as the column labels do not look like numbers, this will also work

% perltab -e 'bemin $m, F(hei)' -z 'say $m'

To do that on the command line without perltab is quite difficult without a LOT of typing, mostly because non-numerical values must be silently skipped but also because $m needed to be initialized properly (for example zero won't work if negative values are present in the data). perltab defines several reasonably mnenmonic functions to handle issues like that transparently.

I believe perltab can be a valuable contribution to CPAN. However perltab would be an unusual contribution to CPAN in that it is designed to be used as a stand-alone command line tool rather than as a library. In fact, is implemented as a plain program rather than a module. Other differences from most CPAN modules is that its bilingual help documentation is written in a simple ad-hoc markup language rather than POD. I started with POD but it did not fit my needs.

By uploading perltab to PREPAN I hope I can get constructive advice on how to move this somewhat atypical contribution into CPAN.

The perltab documention % perltab -h has close to 50 examples of using perltab and all of these are represented in the regression test suite.

paulhorton@github 7 comments

Virt::LXC Manage LXC containers with Perl

The full documentation of the module can be found in the lxc.pod file available on the module repo.

I have some direct questions to ask, but feel free to comment even about points I don't mentioned ;-)

My questions are :

  • How should I name this module ? At the beginning, I was thinking of Linux::Virt::LXC, but it seems that Linux::Virt is a “reserved” namespace for the already existing Linux::Virt module. The same occurs with Sys::Virt. Is thus ok to simply name it Virt::LXC ? I guess not because we lost the notion that this module is only designed to work on Linux, but I don't know what other to choose.

  • My module relies on lxc-* commands that should already be installed on the host. How should I manage the loading of the module in a environment that has those commands missing? Is it a good practice to directly bring the module into a failure (by returning something else than 1 at its importation)?

  • I wrote a (quite messy…) test file that is heavy to run because it has to create real LXC containers on the system that run the tests. Because of that, I choose to put them in the test folder reserved to developers (xt/) is it a good way to do?

  • I am using Log::Any for debugging and monitoring purpose. Is it ok to use it directly in this public module, or should I remove the log management and create a personal wrapper that will manage them? The thing is that Log::Any seems to be quite light and that some users of the lib will probably find it convenient. On the other hand, another group of users will probably be annoyed because they maybe had planned to log stuff differently. :-/

That's all for me! I'm now trying to lean how to manage the deployment with Dist::Zilla, and waiting for your answers. Thank for your help!

spydemon@github 4 comments

Date::Calc::Endpoints Calculate start/end dates for year/qtr/month/week ranges, based on flexible parameters.

NAME

Date::Calc::Endpoints - Generate start/end dates easily, based on type (year, month,...), number of consecutive entities ("4 months"), number of intervals from the current date, and direction (past/future).

VERSION

1.00

SYNOPSIS

use Date::Calc::Endpoints;

my $dr = Date::Calc::Endpoints->new(%params);

my ($start_date,$end_date,$last_date) = $dr->get_dates();

my ($start_date,$end_date,$last_date) = $dr->get_dates(%params);

$dr->set_type([ YEAR | QUARTER | MONTH | WEEK | DAY ]);

$dr->set_intervals(n);

$dr->set_span(n);

$dr->set_sliding_window([ 0 | 1 ]);

$dr->set_direction([ '+' | '-' ]);

$dr->set_start_day_of_week([ MONDAY | TUESDAY | ...]);

$dr->set_start_day_of_month([ 1, 2, 3, ... 28 ]);

$dr->set_start_month_of_year([ 1, 2, 3, ... 12 ]);

$dr->set_today_date('YYYY-MM-DD');

$dr->get_error();

DESCRIPTION

Date::Calc::Endpoints calculates a start/end date based on a interval type, and a number of intervals from the current date. This is often required in running scheduled and ad-hoc reports using the same script, where the desired date range has the requirement of, "7 months ago", or, "5 weeks ago, running Tuesday to Monday".

Three dates are returned for the given interval:

  • First date of the interval
  • First date of the next interval
  • Last date of the interval

Two "end" dates are returned for convenience, as a report using a date+time field may require a query from "2015-10-01 through 2015-11-01", but the title of the report may be, "Output for 2015-10-01 through 2015-10-31".

Date ranges are calculated based on the following parameters:

  • type - the basic time interval for the report [ YEAR | QUARTER | MONTH | WEEK | DAY ] - no default, must be specified

    Note: QUARTER calculates the ranges for (Jan-Mar / Apr-Jun / Jul-Sep / Oct-Dec)

  • intervals - how many "units in the past" (eq, "4 months ago") - default = 1

  • span - number of consecutive units (eq, "5 month window") - default = 1
  • sliding_window - Applicable if span > 1. If sliding_window is set, each interval back will slide by one unit of type. If sliding window is not set, each interval back will slide by (span) units of type. - default = 0
  • direction - If set to "-", each positive value for "intervals" goes further into the past, and each negative value for "intervals" goes further into the future. If set to "+", the opposite applies.
  • start_day_of_week - For type = WEEK, the day which should be used as the first day of the week (SUNDAY, MONDAY, ...) - default = MONDAY
  • start_day_of_month - For type = MONTH, the day which should be used as the start date of the month. Valid values are 1..28. Date::Calc is used for these calculations. If adding/subtracting months, and the day component of the start month is greater than the number of days in the resulting month (ex, "Feb 30"), Date::Calc extends the calculation into the following month ("Mar 2"). To prevent confusion, Date::Calc::Endpoints only supports start_dom of 1 to 28.
  • start_month_of_year - For type = YEAR, the month which should be used as the first day of the year. Valid values are 1..12. This would be applicable for fiscal years, which do not always start with January.
  • today_date - Overrides the current date, typically for development/test purposes.

The current window (intervals = 0) contains the current date.

Illustrations

The following tables illustrate the effect of various values of direction, sliding window, and interval, assuming span = 2. Notice in each case, "interval=1" is one unit away from the one containing the current date (C).

Direction = "-", sliding window = 0
     -3| -2| -1| C | 1 | 2 | 3
    ---|---|---|---|---|---|---
-1)    |   |   |   |   |xxx|xxx
 0)    |   |   |xxx|xxx|   |
 1)    |xxx|xxx|   |   |   |

Direction = "-", sliding window = 1
     -3| -2| -1| C | 1 | 2 | 3
    ---|---|---|---|---|---|---
-1)    |   |   |xxx|xxx|   |
 0)    |   |xxx|xxx|   |   |
 1)    |xxx|xxx|   |   |   |

Direction = "+", sliding window = 0
     -3| -2| -1| C | 1 | 2 | 3
    ---|---|---|---|---|---|---
-1) xxx|xxx|   |   |   |   |
 0)    |   |xxx|xxx|   |   |
 1)    |   |   |   |xxx|xxx|

Direction = "+", sliding window = 1
     -3| -2| -1| C | 1 | 2 | 3
    ---|---|---|---|---|---|---
-1)    |   |xxx|xxx|   |   |
 0)    |   |   |xxx|xxx|   |
 1)    |   |   |   |xxx|xxx|

METHODS

new

Object constructor. Parameters can be set here, or in get_dates, or by set__param_ methods.

  • Arguments: \%parameters

    my ($start, $end, $last) = $dr->new(\%parameters);

  • type => [ YEAR | QUARTER | MONTH | WEEK | DAY ]

    Interval type. No default value - must be specified.

  • intervals => n

    Number of intervals to move back/forth from the current interval. Default = 1.

  • span => n

    Number of type to include in the range. Default = 1.

  • start_day_of_week => [ MONDAY | TUESDAY | WEDNESDAY | ... ]

    For type = WEEK, the day to denote the first day of the week. Default = MONDAY.

  • start_day_of_month => [ 1, 2, 3...28 ]

    For type = MONTH, the day to denote the first day of the month. Default = 1.

  • sliding_window => [ O | 1 ]

    Applicable when span > 1. If sliding_window=1, each successive intervals results in a shift of span (years, months, etc). If sliding_window=0, each successive intervals results in a shift of one (year, month, etc). Default = 0.

  • direction => [ "+" | "-" ]

    If direction="-", intervals progresses further into the past. If direction="+", intervals progresses further into the future. Default = "-".

get_dates

Main method. Returns start_date, end_date, and last_date.

  • Arguments: \%Parameters

    my ($start, $end, $last) = $dr->get_dates(\%parameters);

    Any of the parameters set in new may be set/overridden here.

Accessors

Each of the parameters may be set/restrieved using set__param_ / get__param_ methods.

set_intervals / get_intervals

Interval type: [ YEAR | QUARTER | MONTH | WEEK | DAY ]. No default - must be specified.

set_span / get_span

Overrides the ranges running only one year/quarter/month/week/day at a time. Default = 1.

set_start_day_of_week / get_start_day_of_week

For weekly ranges, defines the starting day to be used for the week, [ MONDAY | TUESDAY | WEDNESDAY | ... ]. Default = Monday.

set_start_day_of_month / get_start_day_of_month

For monthly ranges, defines the starting day to be used for the month. Only supported values are 1-28, as months with less than 31 days may yield results unexpected by the end user. Default = 1.

set_start_month_of_year / get_start_month_of_year

For yearly ranges, defiens the starting month to be used. The starting day is fixed at 1. Default = 1 (January)..

set_today_date / get_today_date

By default, the current date is used. This can be overridden, for development/test purposes. Format must be YYYY-MM-DD.

set_sliding_window / get_sliding_window

Applicable if span > 1. Determines whether successive intervals move an entire span, or just a single amount of type. For instance, if type = MONTH and span = 5, should each successive value of intervals advance one month at a time, or five months at a time. Default = 0 ("five months at a time").

set_direction / get_direction

The direction which successive intervals progresses. This allows for positive values of interval, whether looking into the past, or into the future. To get date ranges which are further into the past, recommend setting direction to "-". If date ranges in the future are required, recommend setting direction to "+". Default = "-". Refer to the Illustrations section for examples.

get_error

Retrieve any errors detected by the object.

clear_error

Reset the error stack

EXAMPLES

Date is 2015-10-10, type = 'MONTH', direction = '-', span = 1. Such a setup would be used for running monthly reports.

Intervals = 0 would be the current month:

my $dr = Date::Calc::Endpoints->new(type => 'MONTH');
my ($start, $end, $last) = $dr->get_dates(intervals => 0);
    (2015-10-01, 2015-11-01, 2015-10-31)

Intervals = 4 would be four months prior to this:

my $dr = Date::Calc::Endpoints->new(type => 'MONTH');
my ($start, $end, $last) = $dr->get_dates(intervals => 4);
    (2015-06-01, 2015-07-01, 2015-06-30)

If "intervals" is a negative number, ranges would be in the future (improbable, but supported):

my $dr = Date::Calc::Endpoints->new(type => 'MONTH');
my ($start, $end, $last) = $dr->get_dates(intervals => -1);
    (2015-11-01, 2015-12-01, 2015-11-30)

Date is 2015-10-10, type = 'MONTH', direction = '-', span = 5. Sliding window now becomes relevant.

Intervals = 1 should still be the most recent, completed period. If sliding_window = 0:

my $dr = Date::Calc::Endpoints->new(type => 'MONTH', span => 5);
my ($start, $end, $last) = $dr->get_dates(intervals => 1);
    (2015-05-01, 2015-10-01, 2015-09-30)

Intervals = 0 will be the next period, starting with the current month:

my $dr = Date::Calc::Endpoints->new(type => 'MONTH', span => 5);
my ($start, $end, $last) = $dr->get_dates(intervals => 0);
    (2015-10-01, 2016-03-01, 2016-02-29)

Now, if sliding window is enabled, intervals = 1 should still be the most recent, completed period:

my $dr = Date::Calc::Endpoints->new(type => 'MONTH', span => 5, sliding_window => 1);
my ($start, $end, $last) = $dr->get_dates(intervals => 1);
    (2015-05-01, 2015-10-01, 2015-09-30)

This time, intervals = 0 will end with the current month:

my $dr = Date::Calc::Endpoints->new(type => 'MONTH', span => 5, sliding_window => 1);
my ($start, $end, $last) = $dr->get_dates(intervals => 0);
    (2015-06-01, 2015-11-01, 2015-10-31)

All parameters can be set at instantiation, set distinctly, or passed in with get_dates.

my $dr = Date::Calc::Endpoints->new(type => 'MONTH', intervals => 1);
my ($start, $end, $last) = $dr->get_dates();
    (2015-09-01, 2015-10-01, 2015-09-30)

$dr->set_intervals(2);
my ($start, $end, $last) = $dr->get_dates();
    (2015-08-01, 2015-09-01, 2015-08-31)

my ($start, $end, $last) = $dr->get_dates(intervals => 3);
    (2015-07-01, 2015-08-01, 2015-07-31)

DIAGNOSTICS

Any errors detected may be retrieved via $dr->get_errors. Errors are accumulated as they are encountered. They are cleared only when $dr-clear_errors> is invoked.

DEPENDENCIES

Class::Accessor

Date::Calc

AUTHOR

T. Olenchuk

LICENSE / COPYRIGHT / DISCLAIMER

This is free software, you may use it and distribute it under the same terms as Perl itself. There is no warranty of any kind, either expressed or implied.

LIMITATIONS

  • The only allowed format for returned dates is 'YYYY-MM-DD'.
  • "Start day-of-month" is only valid only for values 1-28. This was to avoid trying to use last-day-of-month, which becomes problematic for days with less than 31 days. Arguments could be made that, "one month after the last day of January" is Feb 28, or March 3, or even March 4 on a leap year.
  • Any date calculations not supported by Date::Calc are not supported here, such as "3000 years ago".

olenchuk@github 4 comments

IPIP Interface to IPIP.net database

ipip.net database download:http://www.ipip.net/index.html#down

shcabin@github 1 comment

Test::DeepMock Base package for mock factories

Test::DeepMock is a abstract mock factory which injects mocks into @INC so whenever your app requires a package - mock will be loaded. Extremely useful for testing old legacy code.

mykhailokoretskyi@github 0 comments

Plack::App::GzipStatic mimics gzip_static

This is a static file server (most codes are stolen from Plack::App::File) with additional feature gzip_static, known for nginx and Apache.

hkoba@github 0 comments