How to install CRISPRCasFinder (for detection of CRISPRs and cas genes)

https://blogs.perl.org/users/glycine/2024/05/how-to-install-crisprcasfinder-for-detection-of-crisprs-and-cas-genes.html

I need to find the distance between two GPS coordinates. Geo::Calc does this effectively, but it hasn't been updated in over a decade, and, more seriously, it adds a significant startup delay just by loading the module:

root@1c8fb16bd7bb:/app# time perl -e 'use v5.38' real 0m0.005s user 0m0.001s sys 0m0.004s root@1c8fb16bd7bb:/app# time perl -e 'use v5.38; use Geo::Calc' real 0m0.679s user 0m0.631s sys 0m0.048s 

submitted by /u/tyrrminal
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The portions of B::Generate associated with PADOP construction use static variables, and thus are not thread safe.

This release imports that section of Generate.xs into sealed.xs and removes the static variable dependencies.

submitted by /u/joesuf4
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Carp::Object, an object-oriented replacement for Carp and Carp::Clan

https://blogs.perl.org/users/dami/2024/05/carpobject-an-object-oriented-replacement-for-carp-and-carpclan.html

The Perl Toolchain Summit 2024

https://blogs.perl.org/users/paul_johnson/2024/05/the-perl-toolchain-summit-2024.html

I am hopeful someone has done this before as I'm stuck... I have a 3TB disk image file and I am trying to find all the different email addresses that I've used over the past 22 years.

I can use hex editor tools to find them but it takes days to look at the data and pick out even a handful of matches.

I use Perl regularly but I normally scan text files and do non binary file actions. That's easy since I can do a line by line search. But binary seems different.

If I want to search for zeropoint@ (no domain because I've used dozens of ISPs over the years and that's why I am trying to figure this out.) inside the entire 3TB file, what's the best way to do that? I can dump the results to a file and then clean it up but the search part has me stuck

Thank you

submitted by /u/zeropointlabs
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Benchmark::DKbench Perl benchmark suite now supports custom benchmarks.

https://blogs.perl.org/users/dimitrios_kechagias/2024/05/benchmarkdkbench-perl-benchmark-suite-now-supports-custom-benchmarks.html

This week in PSC (146) | 2024-05-02

https://blogs.perl.org/users/psc/2024/05/this-week-in-psc-146-2024-05-02.html

Perl Weekly Challenge 267: Line Count

https://blogs.perl.org/users/laurent_r/2024/05/perl-weekly-challenge-267-line-count.html

Perl Toolchain Summit 2024 - Lisbon Portugal

https://blogs.perl.org/users/chad_exodist_granum/2024/05/perl-toolchain-summit-2024---lisbon-portugal.html

LPW 2024 - Call For Papers and Sponsors

https://blogs.perl.org/users/lpw/2024/05/lpw-2024---call-for-papers-and-sponsors.html

Perl Weekly Challenge 267: Product Sign

https://blogs.perl.org/users/laurent_r/2024/05/perl-weekly-challenge-267-product-sign.html

PTS 2024 - Day 4 - here comes the sun... it's all right!

https://blogs.perl.org/users/leo_lapworth/2024/04/pts-2024---day-4---here-comes-the-sun-its-all-right.html

PTS 2024 - day 2 and 3... the bad days

https://blogs.perl.org/users/leo_lapworth/2024/04/pts-2024---day-2-and-3-the-bad-days.html

Although Benchmark::DKbench is a good overall indicator for generic CPU performance for comparing different systems (especially when it comes to Perl software), the best benchmark is always your own code. Hence, the module now lets you incorporate your own custom benchmarks. You can either have them run together with the default benchmarks, or run only your own set, just taking advantage of the framework (reports, multi-threading, monotonic precision timing, configurable repeats with averages/stdev, calculation of thread scaling etc). Here's an example where I run a couple of custom benchmarks on their own with Benchmark::DKbench:

``` use Benchmark::DKbench;

A simplistic benchmark sub:

sub str_bench { for (1..1000) { my $str = join("", map { chr(97 + rand(26)) } 1..rand(15000)); $str =~ s/a/bd/g; $str =~ tr/b/c/; } }

my %stats = suiterun({ include => 'custom', # Run only my custom benchmarks iter => 5, # Iterations to get an average extra_bench => { custom_bench1 => [&str_bench], # Add one more, just inline this time: custom_bench2 => [sub {my @a=split(//, 'x'x$) for 1..5000}], } }); ``` This will produce a report in STDOUT and also return the results in a hash for a single-thread run. You can also run the benchmarks multi-treaded and then calculate & print the multi/single-thread scalability:

```

If you want to get a count of logical cores:

my $cores = system_identity(1);

my %statsmulti = suite_run({ include => 'custom', threads => $cores, iter => 5, extra_bench => { custom_bench1 => [&str_bench], custom_bench2 => [sub {my @a=split(//, 'x'x$) for 1..5000}], } });

my %scal = calc_scalability(\%stats, \%stats_multi); ```

The report prints results per iteration and also aggregates:

``` Aggregates (5 iterations): Benchmark Avg Time (sec) Min Time (sec) Max Time (sec) custom_bench1: 1.092 1.079 1.107 custom_bench2: 0.972 0.961 0.983 Overall Avg Time (sec): 2.065 2.048 2.080

Aggregates (5 iterations, 10 threads): Benchmark Avg Time (sec) Min Time (sec) Max Time (sec) custom_bench1: 1.534 1.464 1.651 custom_bench2: 1.278 1.225 1.345 Overall Avg Time (sec): 2.812 2.689 2.965 The scalability report summarizes as well: Multi thread Scalability: Benchmark Multi perf xSingle Multi scalability % custom_bench1: 7.12 71

custom_bench2: 7.61 76

DKbench summary (2 benchmarks, 5 iterations, 10 threads): Single: 2.065s Multi: 2.812s Multi/Single perf: 7.36x (7.12 - 7.61) Multi scalability: 73.6% (71% - 76%) ```

The suite normally uses a scoring system which works better than times, so you can set that up by adding reference times to each benchmark, and you can also make the benchmarks return something (checksum etc) to verify results etc, see POD for more.

submitted by /u/dkech
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From the tprc-general Slack channel, Todd Rinaldo wrote yesterday that "Talk Accept, Decline, Waitlist emails have been sent out." See tprc.us for more information about this year's Perl and Raku Conference in Las Vegas, NV.

submitted by /u/talexbatreddit
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Mo utilities for email.

Changes for 0.02 - 2024-04-26T23:02:53+02:00

• Add tests for error parameters.
• Rewrite the tests so that the functional tests are first and then the errors.

PTS 2024 - day 1

https://blogs.perl.org/users/leo_lapworth/2024/04/pts-2024---day-1.html

Perl CPU Benchmark

Changes for 2.6 - 2024-04-25

• Custom benchmark improvements.
• Fix BSD tar xattr.

Code coverage metrics for Perl

Changes for 1.41

• Spelling, linting and formatting changes

load Data::Dumper output, including self-references

Changes for 0.01 - 2024-04-25

Experimental features made easy

Changes for 0.032 - 2024-04-25T22:30:41+01:00

• Add the newly-stable features to stable.pm - extra_paired_delimiters, const_attr, for_list

This week in PSC (145)

https://blogs.perl.org/users/psc/2024/04/this-week-in-psc-145.html

Hi! Asking for a wisdom here...

We have a module that modifies signal handler $SIG{__DIE__} to log information and to die afterwards. Hundreds of scripts relied on this module which worked fine in perl 5.10.1.

Recently we had the opportunity to install several Perl versions but unfortunately a large number of scripts that used to work with Perl 5.10.1 now behave differently:

• Failed in 5.14.4: /home/dev/perl-5.14.4/bin/perl -wc test.pl RECEIVED SIGNAL - S_IFFIFO is not a valid Fcntl macro at /home/dev/perl-5.14.4/lib/5.14.4/File/stat.pm line 41
• Worked without changes in 5.26.3: /home/dev/perl-5.26.3/bin/perl -wc test.pl test.pl syntax OK
• Worked without changes in 5.38.2: /home/dev/perl-5.38.2/bin/perl -wc test.pl test.pl syntax OK

Many of the scripts can only be updated to 5.14.4 due to the huge jumps between 5.10 and 3.58; But we are stuck on that failures.

Was there an internal Perl change in 5.14 which cause the failures but works on other recent versions without any update on the scripts?

Cheerio!

submitted by /u/Longjumping_Army_525
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Perl Weekly Challenge 266: X Matrix

https://blogs.perl.org/users/laurent_r/2024/04/perl-weekly-challenge-266-x-matrix.html

Sanity-check calling context

Changes for 0.04

• (no code changes)
• Switched to MIT license.
• Switched README from POD to Markdown.
• Removed Travis CI.

Sort lines of text by a SortKey module

Changes for 0.001 - 2024-03-07

• First release.

Sort lines of text by a Comparer module

Changes for 0.002 - 2024-03-07

• No functional changes.
• [doc] Mention some related links.

An assortment of date-/time-related CLI utilities

Changes for 0.128 - 2024-03-07

• [clis strftime, strftimeq] Use localtime() instead of gmtime(). We can still show UTC using "TZ=UTC strftime ...".

Perl Weekly Challenge 266: Uncommon Words

https://blogs.perl.org/users/laurent_r/2024/04/perl-weekly-challenge-266-uncommon-words.html

Read Perl’s symbol table programmatically

Changes for 0.11

• (No code changes.)
• Remove Travis CI.
• Change README to Markdown.
• Re-license under the MIT License.

Perl implementation for the Prague Markup Language (PML).

Changes for 2.25 - 2024-04-23T15:11:42Z

• Fix saving relative paths to resource files.

Create a DateTime object from a Genealogy Date

Changes for 0.06 - 2024-04-23T08:28:40Z

• Handle entries which have the French 'Mai' instead of the English 'May' Some messages were printed even in quiet mode Handle '1517-05-04' as '04/05/1517'

Show context around syntax errors and exceptions

Changes for v0.4.0 - 2024-04-23

• fixes
• new features
• improvements
• other