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@heikkil
heikkil / user-rules.xml
Last active Aug 29, 2015
New Plain English rules for LanguageTool 2.7
View user-rules.xml
<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
heikkil / obogrep
Created Apr 21, 2014
grep for obo ontology files
View obogrep
#!/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
heikkil / testing_oo_fasta.pl
Created Feb 7, 2014
Testing simple OOP approach to FASTA parsing
View testing_oo_fasta.pl
#!/usr/bin/env perl
package FastaSeq;
#use Mo qw'build default builder coerce is required';
use Mo;
has id => ();
has descr => ();
has seq => ();
1;
View txt2para.pl
#!/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
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