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lib/Bio/RNA/RNAaliSplit/WrapRscape.pm  view on Meta::CPAN

  }

  $self->_parse_rscape($rscape_out);

  rename $rscape_out, $out;
  rename $rscape_sout, $sout;
}

# parse R-scape output
# canonical R-scape output is expected to look like this:
#  MSA myaln nseq 9 (9) alen 45 (45) avgid 79.51 (79.51) nbpairs 11 (11)
#  contacts  11 (11 bpairs 11 wc bpairs)
#  maxD      8.00
#  mind      1
#  Method Target_E-val [cov_min,conv_max] [FP | TP True Found | Sen PPV F]
#  RAFS    0.05           [-1.00,0.83]    [0 | 3 11 3 | 27.27 100.00 42.86]
#        left_pos       right_pos        score   E-value
# ------------------------------------------------------------
#*	        20	        36	0.83	0.000328218
#*	        21	        35	0.83	0.000328218
#*	        22	        34	0.33	0.0497359

lib/Bio/RNA/RNAaliSplit/WrapRscape.pm  view on Meta::CPAN

sub _parse_rscape {
  my ($self,$out) = @_;
  my $this_function = (caller(0))[3];
  my @buffer = ();
  my $parse1 = 0;
  my $parse2 = 0;
  my $nosbp = 0;
  open my $file, "<", $out or croak "ERROR: [$this_function] Cannot open file $out";
  while(<$file>){
    chomp;
    if (m/^#\s+MSA\s+([a-zA-Z0-9_.|]+)\s+nseq\s+(\d+)\s+\(\d+\)\s+alen\s+(\d+)\s+\(\d+\)\s+avgid\s+(\d+\.\d+)\s+\(\d+\.\d+\)\s+nbpairs\s+(\d+)\s+\(\d+\)/g){
      $self->nseq($2);
      $self->alen($3);
      $self->nbpairs($5);
      $parse1 = 1;
      next;
    }
    if (m/^#\s+([a-zA-Z0-9]+)\s+(\d+\.\d+)\s+\[(\-?\d+\.\d+),(-?\d+\.\d+)\]\s+\[(\d+)\s+\|\s+(\d+)\s+(\d+)\s+(\d+)\s+\|\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\]/g){
      $self->evalue($2);
      $self->FP($5);
      $self->TP($6);