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# -*-CPerl-*- |
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# Last changed Time-stamp: <2017-05-28 17:05:51 mtw> |
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# Bio::RNA::RNAaliSplit::WrapRNAz.pm: A versatile object-oriented |
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# wrapper for RNAz |
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# |
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# Requires RNAz executable available to the Perl interpreter. |
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# This package contains code fragments from the original RNAz Perl module |
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package Bio::RNA::RNAaliSplit::WrapRNAz; |
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use version; our $VERSION = qv('0.05'); |
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use Carp; |
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use Data::Dumper; |
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use Moose; |
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use Path::Class; |
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use IPC::Cmd qw(can_run run); |
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use File::Path qw(make_path); |
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#use diagnostics; |
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my ($rnaz,$oodir); |
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has 'basename' => ( |
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is => 'rw', |
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isa => 'Str', |
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predicate => 'has_basename', |
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documentation => q(Set this to override output basename), |
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); |
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has 'P' => ( |
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is => 'rw', |
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isa => 'Num', |
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init_arg => undef, |
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documentation => q(SVM RNA-class probability), |
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); |
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has 'z' => ( |
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is => 'rw', |
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isa => 'Num', |
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init_arg => undef, |
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documentation => q(Mean z-score), |
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); |
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has 'sci' => ( |
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is => 'rw', |
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isa => 'Num', |
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init_arg => undef, |
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documentation => q(Structure conservation index), |
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); |
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with 'FileDirUtil'; |
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with 'Bio::RNA::RNAaliSplit::Roles'; |
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sub BUILD { |
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my $self = shift; |
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my $this_function = (caller(0))[3]; |
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confess "ERROR [$this_function] \$self->ifile not available" |
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unless ($self->has_ifile); |
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$rnaz = can_run('RNAz') or |
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croak "ERROR [$this_function] RNAz not found"; |
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unless($self->has_odir){ |
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unless($self->has_dirnam){self->dirnam("as")} |
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$self->odir( [$self->ifile->dir,$self->dirnam] ); |
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} |
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$oodir = $self->odir->subdir("rnaz"); |
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my @created = make_path($oodir, {error => \my $err}); |
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confess "ERROR [$this_function] could not create output directory $self->oodir" |
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if (@$err); |
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$self->set_ifilebn; |
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$self->run_rnaz(); |
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} |
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sub run_rnaz { |
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my $self = shift; |
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my $this_function = (caller(0))[3]; |
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my ($rnaz_outfilename,$rnaz_out); |
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if ($self->has_basename){$rnaz_outfilename = $self->basename.".rnaz.out"} |
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elsif ($self->has_ifilebn){$rnaz_outfilename = $self->ifilebn.".rnaz.out"} |
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else{$rnaz_outfilename = "rnaz.out"} |
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$rnaz_out = file($oodir,$rnaz_outfilename); |
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open my $fh, ">", $rnaz_out; |
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my $rnaz_cmd = $rnaz." -l -d < ".$self->ifile; |
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my ( $success, $error_message, $full_buf, $stdout_buf, $stderr_buf ) = |
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run( command => $rnaz_cmd, verbose => 0 ); |
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if( !$success ) { |
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print STDERR "ERROR [$this_function] Call to $rnaz unsuccessful\n"; |
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print STDERR "ERROR: this is what the command printed:\n"; |
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print join "", @$full_buf; |
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croak $!; |
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} |
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my $stdout_buffer = join "", @$stdout_buf; |
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my @out = split /\n/, $stdout_buffer; |
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foreach my $line( @out){print $fh $line,"\n"} |
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close($fh); |
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$self->_parse_rnaz($stdout_buffer); |
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} |
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# parse RNAz output |
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sub _parse_rnaz { |
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my ($self,$rnaz) = @_; |
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my $this_function = (caller(0))[3]; |
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my @rnaz=split(/^/, $rnaz); |
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my ($N,$identity,$columns,$decValue,$P,$z,$sci,$energy,$strand, |
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$covariance,$combPerPair,$meanMFE,$consensusMFE,$consensusSeq, |
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$consensusFold, $GCcontent, $ShannonEntropy); |
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my @aln=(); |
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foreach my $i (0..$#rnaz){ |
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my $line=$rnaz[$i]; |
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$identity=$1 if ($line=~/Mean pairwise identity:\s*(-?\d+.\d+)/); |
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$N=$1 if ($line=~/Sequences:\s*(\d+)/); |
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if ($line=~/Reading direction:\s*(forward|reverse)/){ |
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$strand=($1 eq 'forward')?'+':'-'; |
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} |
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$columns=$1 if ($line=~/Columns:\s*(\d+)/); |
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$decValue=$1 if ($line=~/SVM decision value:\s*(-?\d+.\d+)/); |
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$P=$1 if ($line=~/SVM RNA-class probability:\s*(-?\d+.\d+)/); |
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$z=$1 if ($line=~/Mean z-score:\s*(-?\d+.\d+)/); |
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$sci=$1 if ($line=~/Structure conservation index:\s*(-?\d+.\d+)/); |
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$energy=$1 if ($line=~/Energy contribution:\s*(-?\d+.\d+)/); |
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$covariance=$1 if ($line=~/Covariance contribution:\s*(-?\d+.\d+)/); |
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$combPerPair=$1 if ($line=~/Combinations\/Pair:\s*(-?\d+.\d+)/); |
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$consensusMFE=$1 if ($line=~/Consensus MFE:\s*(-?\d+.\d+)/); |
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$meanMFE=$1 if ($line=~/Mean single sequence MFE:\s*(-?\d+.\d+)/); |
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$GCcontent=$1 if ($line=~/G\+C content:\s(\d+.\d+)/); |
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$ShannonEntropy=$1 if ($line=~/Shannon entropy:\s*(\d+.\d+)/); |
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0
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if ($line=~/^>/){ |
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chomp($rnaz[$i+1]); |
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chomp($rnaz[$i+2]); |
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if ($line=~/^>consensus/){ |
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$consensusSeq=$rnaz[$i+1]; |
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$consensusFold=substr($rnaz[$i+2],0,length($rnaz[$i+1])); |
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last; |
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} else { |
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if ($line=~/>(.*?) (\d+) (\d+) (\+|\-) (\d+)/){ |
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push @aln, {name=>$1, |
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start=>$2, |
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end=>$2+$3, |
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strand=>$4, |
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fullLength=>$5, |
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seq=>$rnaz[$i+1], |
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fold=>substr($rnaz[$i+2],0,length($rnaz[$i+1]))}; |
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$i+=2; |
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} elsif ($line=~/^(.*)\/(\d+)-(\d+)$/){ |
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push @aln, {name=>$1, |
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start=>$2, |
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end=>$3, |
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strand=>$strand, |
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fullLength=>'', |
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seq=>$rnaz[$i+1], |
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fold=>substr($rnaz[$i+2],0,length($rnaz[$i+1]))}; |
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$i+=2; |
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} |
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} |
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} |
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} |
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159
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0
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$self->P($P); |
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$self->z($z); |
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$self->sci($sci); |
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} |
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164
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1; |