#!/Users/distiller/project/miniconda/conda-bld/meme_1591690490148/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/perl

use strict;
use warnings;

use Fcntl qw(O_CREAT O_WRONLY O_TRUNC);
use Getopt::Long;
use Pod::Usage;

=head1 NAME

fasta-re-match - reports all matches to a IUPAC DNA motif, 1 per line.

=head1 SYNOPSIS

fasta-re-match [options] <IUPAC DNA Motif>

 Options:
  -norc                     Only find matches to motifs in the given strand
  -erase <IUPAC DNA Motif>  erases this motif before finding matches; 
                            repeatable; order matters!
  -help                     prints this help message

 Reads sequences from standard input.

 Writes to standard output tab separated (space padded) columns:
 <matching sequence> <strand +-> <line number> <column number> <sequence offset> <sequence name>

 If you are trying to recreate DREME motif sites note that DREME erases 
 previously found motifs so you will have to use the -erase option for any but 
 the first motif, like:
 fasta-re-match -erase CCMCRCCC TTATCW < sample-dna-Klf1.fa

 If you want a count of sites try piping the output to "wc -l" like:
 fasta-re-match CCMCRCCC < sample-dna-Klf1.fa | wc -l

 If you want only one of the columns try piping the output to "cut -f <num>" like:
 fasta-re-match CCMCRCCC < sample-dna-Klf1.fa | cut -f 1

=cut

my $help = 0; #FALSE
my $norc = 0; #FALSE
my @erase = ();
my $iupac = undef;
my @erase_re = ();
my $motif_re = undef;
my $motif_given_re = undef;

GetOptions(
  "norc" => \$norc,
  "erase=s" => \@erase,
  "help|?" => \$help
) or pod2usage(2);
pod2usage(1) if ($help);
($iupac) = @ARGV;
# check and create erasure motif REs
for (my $i = 0; $i < scalar(@erase); $i++) {
  $erase[$i] = uc($erase[$i]);
  pod2usage('Value "'. $erase[$i]. '" is invalid for option erase '.
    '(non IUPAC DNA characters)') if ($erase[$i] =~ /[^ACGTRYSWKMBDHVN]/);
  push(@erase_re, &iupac_re($erase[$i], $norc));
}
# check and create search motif RE
pod2usage("No motif given") unless ($iupac);
$iupac = uc($iupac);
pod2usage("Non IUPAC DNA characters") if ($iupac =~ /[^ACGTRYSWKMBDHVN]/);
$motif_re = &iupac_re($iupac, $norc);
$motif_given_re = &iupac_re($iupac, 1);

my $line;
my $seq;
my $id;
my @pos = ();
my $in_seq = 0; #FALSE
my $lineno = 1;

while ($line = <STDIN>) {
  if ($line =~ m/^>(\S+)/) {
    &print_matches();
    $id = $1;
    $in_seq = 1; #TRUE
    @pos = ();
    $seq = '';
  } else {
    if ($in_seq) {
      while ($line =~ /(\S+)/g) {
        push(@pos, [length($seq), $lineno, $-[0]]);
        $seq .= $1;
      }
    }
  }
  $lineno++;
}
&print_matches();
pod2usage("Empty sequences file") unless $in_seq;
exit(0);

sub print_matches {
  return unless $in_seq;
  # erase any requested motifs
  for (my $i = 0; $i < scalar(@erase_re); $i++) {
    my $re = $erase_re[$i];
    my $sub = 'N' x length($erase[$i]);
    $seq =~ s/$re/$sub/g;
  }
  while ($seq =~ /$motif_re/g) {
    my $match = $1;
    my $offset = $-[0];
    my ($line, $col) = &lookup_pos($offset);
    my $strand = $match =~ m/^$motif_given_re$/ ? '+' : '-';
    printf("%s\t%s\t%4d\t%3d\t%5d\t%s\n", $match, $strand, $line, $col, $offset, $id);
  }
}

sub lookup_pos {
  my ($target) = @_;
  my $min = 0;
  my $max = scalar(@pos)-1;
  while ($min < $max) {
    use integer;
    my $mid = ($min + $max) / 2;
    if ($pos[$mid]->[0] > $target) {
      $max = $mid - 1;
    } elsif ($pos[$mid+1]->[0] <= $target) {
      $min = $mid + 1;
    } else {
      $min = $mid;
      $max = $mid;
    }
  }
  my @info = @{$pos[$min]};
  return ($info[1], $info[2] + ($target - $info[0]) + 1);
}

sub iupac_to_bracket {
  my ($in) = @_;
  $in =~ s/A/[A]/g;
  $in =~ s/C/[C]/g;
  $in =~ s/G/[G]/g;
  $in =~ s/T/[T]/g;

  $in =~ s/N/[ACGT]/g;

  $in =~ s/V/[ACG]/g;
  $in =~ s/H/[ACT]/g;
  $in =~ s/D/[AGT]/g;
  $in =~ s/B/[CGT]/g;

  $in =~ s/M/[AC]/g;
  $in =~ s/K/[GT]/g;
  $in =~ s/W/[AT]/g;
  $in =~ s/S/[GC]/g;
  $in =~ s/Y/[CT]/g;
  $in =~ s/R/[AG]/g;

  $in =~ s/A/Aa/g;
  $in =~ s/C/Cc/g;
  $in =~ s/G/Gg/g;
  $in =~ s/T/TtUu/g;

  return $in;
}

sub iupac_re {
  my ($orig, $norc) = @_;
  my $re = &iupac_to_bracket($orig);
  unless ($norc) {
    my $revc = reverse($orig);
    $revc =~ tr/ACGTRYSWKMBDHVN/TGCAYRSWMKVHDBN/;
    $re = $re . '|' . &iupac_to_bracket($revc);
  }
  return qr/($re)/;
}
1;
