standage

#!/usr/bin/env perl

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
# 
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR

standage

#!/usr/bin/env perl

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
# 
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
# 
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

standage

#!/usr/bin/env bash

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
# 
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
# 
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

standage

#!/usr/bin/env perl
use strict;

while(my $line = <STDIN>)
{
  chomp($line);
  my @values = split(/,/, $line);

  my $page = sprintf("%s/%d-%d.html", $values[0], $values[1], $values[2]);
  my $cds_match_coef = $values[33];

standage

#!/usr/bin/env bash
# Usage: bash augustus-gff3-groom.sh genes-before.gff3 > genes-after.gff3

sed $'s/\ttranscript\t/\tmRNA\t/' < $1 | grep -v $'\tintron\t'

standage

#!/usr/bin/env perl

# Copyright (c) 2010-2011, Daniel S. Standage <daniel.standage@gmail.com>
# 
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
# 
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

standage

#!/usr/bin/env bash

# Copyright (c) 2013, Daniel S. Standage <daniel.standage@gmail.com>
# 
# Permission to use, copy, modify, and/or distribute this software for any
# purpose with or without fee is hereby granted, provided that the above
# copyright notice and this permission notice appear in all copies.
# 
# THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
# WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF

standage

#!/usr/bin/env perl
# pe-uniq.pl: a script to process ParsEval output and determine unmatched genes;
# i.e., reference genes for which there are no overlapping prediction genes, and
# vice versa; this script expects ParsEval output in text format
#
# Usage: perl pe-uniq.pl < pe-out.txt > uniq-genes.txt
use strict;

my $locusmatch = quotemeta("|---- Locus:");
while(my $line = <STDIN>)

standage

#!/usr/bin/env perl
use strict;
use Bio::SeqIO;

my $usage = "perl $0 seqs.fasta < coords.csv > subseqs.fasta # coords.csv file is 3 comma-delimited values: seqid, start, and end";
my $seqfile = shift(@ARGV) or die("Usage: $usage");

# Load sequences into memory
my %seqs;
my $seqinput = Bio::SeqIO->new( "-file" => $seqfile, "-format" => "Fasta" );

standage

#!/usr/bin/env perl
use strict;
 
$/ = ">";
<STDIN>; # Discard "junk", if any, at beginning of the file.
 
my @sequencelengths;
my $gccontent = 0;
my $atcontent = 0;
my $combinedlength = 0;