heikkil

#!/usr/bin/env perl

package FastaSeq;
#use Mo qw'build default builder coerce is required';
use Mo;
has id => ();
has descr => ();
has seq => ();
1;

heikkil

#!/usr/bin/env perl

=head1 NAME

obogrep - grep obo entries with a string

=head1 SYNOPSIS

B<obogrep> [B<--version> | [B<-?|-h|--help>] | [B<-g|--debug>] |
  [B<-v|--invert-match>] | [B<-c|--count>] |query obofile

heikkil

<category name="Redundant Phrases" type="style">

  <!-- main source http://en.wikipedia.org/wiki/List_of_plain_English_words_and_phrases -->
  <!-- some rules belonging to other categories included -->
  <!-- xxx marks optional edge tokens that cause an error if uncommented -->

  <rule id="ABUNDANCE" name="abundance">
    <pattern>
      <token>abundance</token>
    </pattern>

heikkil

          "
        _c_enter  _q_uote     _e_macs-lisp    _L_aTeX:
        _l_atex   _e_xample   _p_erl          _i_ndex:
        _a_scii   _v_erse     _P_erl tangled  _I_NCLUDE:
        _s_rc     ^ ^         plant_u_ml      _H_TML:
        _h_tml    ^ ^         ^ ^             _A_SCII:
        "

          ("e" (progn (hot-expand "<s") (insert "emacs-lisp") (forward-line)))
          ("p" (progn (hot-expand "<s") (insert "perl") (forward-line)))

heikkil

#!/usr/bin/env perl

# Turn consecutive non-empty lines of plain text into paragraphs

local $/ = "\n\n";    #paragraph separator

while (<>) {
  chomp($_);

  # Replace newlines inside paragraphs by spaces and remove multiple spaces

heikkil

#!/usr/bin/env perl
use Modern::Perl;
use File::Find;
use Getopt::Long;

use constant PROGRAMME_NAME => 'orphan_raw';
use constant VERSION => '0.2';

GetOptions(
    'v|version'    => sub{ print PROGRAMME_NAME, ", version ", VERSION, "\n";

heikkil

#!/usr/bin/env perl
use Modern::Perl;
use File::Find;
use Getopt::Long;

use constant PROGRAMME_NAME => 'raw_copy';
use constant VERSION => '0.2';

GetOptions(
    'v|version'    => sub{ print PROGRAMME_NAME, ", version ", VERSION, "\n";

heikkil

;; mod from http://blog.binchen.org/posts/use-ivy-mode-to-search-bash-history.html
(require 'dash)
(defun counsel-yank-fish-history ()
  "Yank the fish history"
  (interactive)
  (let (hist-cmd collection val)
    (shell-command "history -r") ; reload history
    (setq collection
          (nreverse
           (split-string (with-temp-buffer (insert-file-contents (file-truename "~/.config/fish/fish_history"))

heikkil

#!/bin/sh
# ~/bin/feh-remove.sh
DIR=`dirname "$1"`
if [ ! -d $DIR/removed ]; then
    mkdir $DIR/removed
fi;
mv "$1" $DIR/removed

heikkil

#!/bin/sh
# ~/bin/feh-copy.sh
DIR=`dirname "$1"`
if [ ! -d $DIR/copied ]; then
    mkdir $DIR/copied
fi;
cp "$1" $DIR/copied