setup and run PIPS to identify Putative Pathogenicity Islands

Recently I need to do PAI search using PIPS, after going throught all the little traps, I think it worth to write the whole process down.

  1. follow the README instructions to install hammer and tRNA-scan. Maybe you want to change the default prefix of INSTALL derectory

  2. Theoretically, it should be good enough to run, but you’ll definitely be stuck at some point. OK, here are the tricks to try below

  3. replace gbk2embl.pl with a new one, such as this:

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

    if (@ARGV != 2) {    die "USAGE: gb2embl.pl <in.gbk> <out.embl>\n"; }

    my $seqio = Bio::SeqIO->new('-format' => 'genbank', '-file' => "$ARGV[0]");
    my $seqout = new Bio::SeqIO('-format' => 'embl', '-file' => ">$ARGV[1]");
    while( my $seq = $seqio->next_seq) {
      $seqout->write_seq($seq)
    }

For the last step, modify mergfiles.pl. change for e.g. %hash2->{$chave} to $hash2{$chave}, note that a couple of similar syntax mistake in this script.