glycine

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• Posted Reading sequences from FASTA format alignment by Bio::Perl to glycine

  Show code for TL;DR:

  use Bio::AlignIO;
  
  my $in = Bio::AlignIO->new(
  
         -file   => $inputfilename ,
  
         -format => 'fasta',
  
       );
  
  while ( my $aln = $in->next_aln() ) { 
  
      foreach my $seq ($aln->each_seq) {
  
          ...; # do some th…

• Commented on Integrated Inconsistencies.
  I also confused at coordinate start from different forward:) your work is amazing, I do not think this before!...
• Commented on Scalar Context: Lists Versus Arrays
  I just interesting about why we have this feature, was it useful in old time?...
• Commented on Strawberry Perl
  before click, I expected this is news of strawberry perl haha. thanks for your article, I usually want this, but never really resolved it :)...
• Commented on The File Access Operators: To Use, or Not to Use
  I just never hear this before...in another way, I do not expect that my computer will lie to me:(...
• Commented on My Favorite Warnings: <code>shadow</code>
  the name is shadow! I expected it is something like mask before hahaha...
• Commented on JavaScript Supported Web Scraping using Perl and Selenium
  thank you! I usually hope understand how to do this and preparing using another language, but perl can do it:)...
• Commented on My Favorite Warnings: <code>experimental</code>
  thanks for interesting historical detail, I did not hear this before....
• Commented on berrybrew version 1.36 released!
  thank you, I had updated it:) p.s. the cmd open from berrybrew GUI looks like differ to cmd which open from start menu(former have black title line), but it do not bother me on anything, so I guess it is...
• Commented on My Favorite Warnings: <code>redefine</code>
  I never think about this ! if keep a reference of a subroutine, even changing the subroutine that the name refer to, it still keep exist. this is suprise....
• Commented on I try match syntax using Syntax::Keyword::Match
  Is this mean we will discard now experimental switch sytax? this looks like useful, thank you:)...
• Commented on My Favorite Warnings: <code>exiting</code>
  I do not trigger it ever, even do not know it exists, thank you :)...
• Commented on How to show UTF-8 at the Windows command prompt
  last time I search how to change code page to utf8, I get warning about windows utf8 code pagehave problem...maybe I need to try ot again....
• Commented on Monthly Report - August
  congraduate!...
• Commented on My Favorite Warnings: once
  before I only know this warining dispaly for only declare variable... I don't connect them together...
• Commented on A dream realized
  wow...most of example use scalar attribute, I don't know this!...
• Commented on Random Thought: Exposure of Perl in the Academic Circles
  yes, python abosolutely more favorite in science now. write a new package by python? contain python in your title! R? maybe just imply it in your package name... there still are a lot of perl leave in the old software,...
• Commented on Tau Station considered Dangerous: Game Review
  sounds like very fun!...
• Commented on berrybrew version 1.34 released!
  Thanks for your work! I install berrybrew first three days ago, it is so convenient and small UI is so cute :)...
• Commented on Let's be friend ...
  oops, I mean actually good, sorry for my silly English...
• Commented on Let's be friend ...
  For me, your work make Perl and Raku looks like have very nice relationship....

Comment Threads

• brian d foy commented on Scalar Context: Lists Versus Arrays

  There's also the perlfaq4 answer to "What is the difference between a list and an array?" https://perldoc.perl.org/perlfaq4#What-is-the-difference-between-a-list-and-an-array?

• lowjoe commented on Integrated Inconsistencies.

  So I then took over Algorithm::Line::Bresenham, and found the original code appeared to take the y-coordinate before the x-coordinate...blasphemy

  And you changed it, breaking everybody's code who was using it, without even a mention in the docs nor changelog (which doesn't even exist). There's a strong tradition in the Perl community to support backwards compatibility. You could have added new functions (e.g. linex, circlex) that use the new argument order, and you wouldn't be inconveniencing users.

• lowjoe commented on Integrated Inconsistencies.

  (The first paragraph of my previous reply was supposed to blockquoted, but guess my html tags weren't applied)

• Aristotle commented on Integrated Inconsistencies.

  guess my html tags weren't applied

  They were, but you used <quote> (which isn’t a thing, and which the tag filter therefore doesn’t permit) rather than <blockquote>. I’ve fixed that for you.

• Saif commented on Integrated Inconsistencies.

  I did change the code, so it looks better (i.e. x come before the y) , output is not changed, and it will work either way. The output points' x-y order will match the the points input, so old code do not need to be altered. Secondly I have checked whether any one else uses it: according to the original author whom I have been in contact with, it is esoteric enough that nobody else uses it. But I agree I should have mentioned it in the pod. will do so in the next iteration.