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

#!/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

#!/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

# 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