New upstream version 3.0.6+dfsg

#! /usr/bin/perl

use IO::String;

use Getopt::Long;

#use Data::Dumper;

use lib '../lib';

use Bio::Tools::PSort::Report::Formatter;

use Bio::Tools::PSort;

use Bio::SeqIO;

use Bio::Tools::PSort::Constants qw(:all);

use Getopt::Long;

use Data::Dumper;

use strict;

our $ENV;

  my $psort_analysis = 'psort';

  my $psort_output = 'bayes';

  my $root = '/usr/local/psortb-3.0';

  my $blastdir = '/usr/local/bio/blast';

  my $root = '/usr/local/psortb3';

  my $blastdir = '/usr/local/pkg/blast-2.2.26//bin';

  my $pftools = '/usr/local/bin/';

  my $pfscan_module = 'Profile';

      die "We should never be here.\n";

    }

  } else {

    # Create a new PSort object.

    print(STDERR "* Using \"$server\" as remote PSort server\n")

  # Figure out whether or not we're getting the sequences from a file or from

  # STDIN and open up a Bio::SeqIO on it.

  my $seqfh;

  if($fname) {

    if((-f $fname) && (-r $fname)) {

      print(STDERR "* Reading sequences from file \"$fname\"\n") if($verbose);

      open(SEQS, $fname) || die("Error: open $fname: $!\n");

      $sio = new Bio::SeqIO(-fh => \*SEQS, -format => $format);

      $seqfh = make_seq_input_uppercase($fname);

    } else {

      die("Error: file \"$fname\" doesn't exist or isn't readable\n");

    }

  } else {

    print(STDERR "* Reading sequences from STDIN\n") if($verbose);

    $sio = new Bio::SeqIO(-fh => \*STDIN, -format => $format);

    $seqfh = make_seq_input_uppercase();

  }

  $sio = new Bio::SeqIO(-fh => $seqfh, -format => $format);

  # Ready for prime time - go forth and PSort.

  my $format = new Bio::Tools::PSort::Report::Formatter();

  }

  print($format->format($output, {-cutoff => $cutoff, -gram => $gram, -mcutoff => $divergent, -psort => $psort, -skiplocalizations => \@skippedlocalizations}, @reps));

}

sub make_seq_input_uppercase {

    my $fname = shift;

    my $seqinput;

    if (defined $fname) {

      open(SEQS, $fname) || die("Error: open $fname: $!\n");

      #$seqinput = <SEQS>;

      $seqinput = do { local $/; <SEQS> };

    } 

    else {

      $seqinput = <>;

    }

    # hack to convert sequences (not headers) to uppercase (lowercase 

    # seems to bring back no psortb results)

    my @seqs2uc = split(">", $seqinput);

    shift(@seqs2uc); # remove blank first element (after doing split on > where > is the first character)

    my $uc_seqs;

    foreach my $header_seq (@seqs2uc) {

      my ($h1, $s1) = split(/[\n\r]+/, $header_seq, 2);

      if ($s1 =~ /[a-z]/) {

        $s1 = uc($s1);

      }

      $uc_seqs .= ">$h1\n$s1";

    }

    my $seqfh = new IO::String($uc_seqs);

    return($seqfh);

}