Here's a #BioPerl blast from the past @hyphaltip - https://github.com/OBF/wp-content/blob/gh-pages/uploads/2006/01/bioperl_graffiti.jpg
(Spotted while working with @gedankenstuecke et al on the trial @OpenBio website migration from WordPress to Hugo on GitHub Pages)
Wrapping over #hmmer http://hmmer.org/ made me appreciate AUTOLOAD in #perl @Perl
The actual code I had to write was minimal , i.e. about 23 lines in the pm file and ~85 in the alienfile, but it ended up "containerizing" (inside perlbrew) all 41 programs of the HMMER and EASEL suites #bioinformatics
#Github repo:
https://github.com/chrisarg/alien-seqalignment-hmmer3
#cpan:
https://metacpan.org/pod/Alien::SeqAlignment::hmmer3
#bioperl relevant modules:
https://metacpan.org/pod/Bio::Tools::Run::Hmmer
https://metacpan.org/pod/Bio::Index::Hmmer
Great start for building one's own programs.
The beauty, succinctness & speed of #bioperl #perl
(creating and accessing an index of 191,106 sequences ~ 275MB of biological (human #cDNA and #ncRNA) sequence data
5 sec to create the index (using BerkeleyDB), and 12 sec to transverse the sequence data
#bioinformatics @Perl
(Code in alt text of the left image edited to fit the character limit)
New release: AI-TensorFlow-Libtensorflow-0.0.6 https://metacpan.org/release/ZMUGHAL/AI-TensorFlow-Libtensorflow-0.0.6
---
This adds an example of using the Enformer model for gene expression prediction with #PDL and #BioPerl.
Peter Cock
Christos Argyropoulos MD, PhD
Zaki