jpayne@69: #!/usr/bin/env perl
jpayne@69: 
jpayne@69: #-------------------------------------------------------------------------------
jpayne@69: #   Programmer: Adam M Phillippy, University of Maryland
jpayne@69: #         File: dnadiff
jpayne@69: #         Date: 11 / 29 / 06
jpayne@69: #
jpayne@69: #   Try 'dnadiff -h' for more information.
jpayne@69: #
jpayne@69: #-------------------------------------------------------------------------------
jpayne@69: 
jpayne@69: use lib "/mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts";
jpayne@69: use Foundation;
jpayne@69: use File::Spec::Functions;
jpayne@69: use strict;
jpayne@69: 
jpayne@69: my $BIN_DIR = "/mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23";
jpayne@69: my $SCRIPT_DIR = "/mnt/c/Users/crash/Documents/BobLiterman/CSP2_Galaxy/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/mummer-3.23/scripts";
jpayne@69: 
jpayne@69: my $VERSION_INFO = q~
jpayne@69: DNAdiff version 1.3
jpayne@69:     ~;
jpayne@69: 
jpayne@69: my $HELP_INFO = q~
jpayne@69:   USAGE: dnadiff  [options]  <reference>  <query>
jpayne@69:     or   dnadiff  [options]  -d <delta file>
jpayne@69: 
jpayne@69:   DESCRIPTION:
jpayne@69:     Run comparative analysis of two sequence sets using nucmer and its
jpayne@69:     associated utilities with recommended parameters. See MUMmer
jpayne@69:     documentation for a more detailed description of the
jpayne@69:     output. Produces the following output files:
jpayne@69: 
jpayne@69:     .report  - Summary of alignments, differences and SNPs
jpayne@69:     .delta   - Standard nucmer alignment output
jpayne@69:     .1delta  - 1-to-1 alignment from delta-filter -1
jpayne@69:     .mdelta  - M-to-M alignment from delta-filter -m
jpayne@69:     .1coords - 1-to-1 coordinates from show-coords -THrcl .1delta
jpayne@69:     .mcoords - M-to-M coordinates from show-coords -THrcl .mdelta
jpayne@69:     .snps    - SNPs from show-snps -rlTHC .1delta
jpayne@69:     .rdiff   - Classified ref breakpoints from show-diff -rH .mdelta
jpayne@69:     .qdiff   - Classified qry breakpoints from show-diff -qH .mdelta
jpayne@69:     .unref   - Unaligned reference IDs and lengths (if applicable)
jpayne@69:     .unqry   - Unaligned query IDs and lengths (if applicable)
jpayne@69: 
jpayne@69:   MANDATORY:
jpayne@69:     reference       Set the input reference multi-FASTA filename
jpayne@69:     query           Set the input query multi-FASTA filename
jpayne@69:       or
jpayne@69:     delta file      Unfiltered .delta alignment file from nucmer
jpayne@69: 
jpayne@69:   OPTIONS:
jpayne@69:     -d|delta        Provide precomputed delta file for analysis
jpayne@69:     -h
jpayne@69:     --help          Display help information and exit
jpayne@69:     -p|prefix       Set the prefix of the output files (default "out")
jpayne@69:     -V
jpayne@69:     --version       Display the version information and exit
jpayne@69:     ~;
jpayne@69: 
jpayne@69: 
jpayne@69: my $USAGE_INFO = q~
jpayne@69:   USAGE: dnadiff  [options]  <reference>  <query>
jpayne@69:     or   dnadiff  [options]  -d <delta file>
jpayne@69:     ~;
jpayne@69: 
jpayne@69: 
jpayne@69: my @DEPEND_INFO =
jpayne@69:     (
jpayne@69:      "$BIN_DIR/delta-filter",
jpayne@69:      "$BIN_DIR/show-diff",
jpayne@69:      "$BIN_DIR/show-snps",
jpayne@69:      "$BIN_DIR/show-coords",
jpayne@69:      "$BIN_DIR/nucmer",
jpayne@69:      "$SCRIPT_DIR/Foundation.pm"
jpayne@69:      );
jpayne@69: 
jpayne@69: my $DELTA_FILTER = "$BIN_DIR/delta-filter";
jpayne@69: my $SHOW_DIFF = "$BIN_DIR/show-diff";
jpayne@69: my $SHOW_SNPS = "$BIN_DIR/show-snps";
jpayne@69: my $SHOW_COORDS = "$BIN_DIR/show-coords";
jpayne@69: my $NUCMER = "$BIN_DIR/nucmer";
jpayne@69: 
jpayne@69: my $SNPBuff         = 20;            # required buffer around "good" snps
jpayne@69: my $OPT_Prefix      = "out";         # prefix for all output files
jpayne@69: my $OPT_RefFile;                     # reference file
jpayne@69: my $OPT_QryFile;                     # query file
jpayne@69: my $OPT_DeltaFile;                   # unfiltered alignment file
jpayne@69: my $OPT_ReportFile  = ".report";     # report file
jpayne@69: my $OPT_DeltaFile1  = ".1delta";     # 1-to-1 delta alignment
jpayne@69: my $OPT_DeltaFileM  = ".mdelta";     # M-to-M delta alignment
jpayne@69: my $OPT_CoordsFile1 = ".1coords";    # 1-to-1 alignment coords
jpayne@69: my $OPT_CoordsFileM = ".mcoords";    # M-to-M alignment coords
jpayne@69: my $OPT_SnpsFile    = ".snps";       # snps output file
jpayne@69: my $OPT_DiffRFile   = ".rdiff";      # diffile for R
jpayne@69: my $OPT_DiffQFile   = ".qdiff";      # diffile for Q
jpayne@69: my $OPT_UnRefFile    = ".unref";     # unaligned ref IDs and lengths
jpayne@69: my $OPT_UnQryFile    = ".unqry";     # unaligned qry IDs and lengths
jpayne@69: 
jpayne@69: my $TIGR;  # TIGR Foundation object
jpayne@69: 
jpayne@69: 
jpayne@69: sub RunAlignment();
jpayne@69: sub RunFilter();
jpayne@69: sub RunCoords();
jpayne@69: sub RunSNPs();
jpayne@69: sub RunDiff();
jpayne@69: sub MakeReport();
jpayne@69: 
jpayne@69: sub FastaSizes($$);
jpayne@69: 
jpayne@69: sub FileOpen($$);
jpayne@69: sub FileClose($$);
jpayne@69: 
jpayne@69: sub GetOpt();
jpayne@69: 
jpayne@69: 
jpayne@69: #--------------------------------------------------------------------- main ----
jpayne@69:  main:
jpayne@69: {
jpayne@69:     GetOpt();
jpayne@69: 
jpayne@69:     RunAlignment() unless defined($OPT_DeltaFile);
jpayne@69:     RunFilter();
jpayne@69:     RunCoords();
jpayne@69:     RunSNPs();
jpayne@69:     RunDiff();
jpayne@69:     MakeReport();
jpayne@69: 
jpayne@69:     exit(0);
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #------------------------------------------------------------- RunAlignment ----
jpayne@69: # Run nucmer
jpayne@69: sub RunAlignment()
jpayne@69: {
jpayne@69:     print STDERR "Building alignments\n";
jpayne@69:     my $cmd = "$NUCMER --maxmatch -p $OPT_Prefix $OPT_RefFile $OPT_QryFile";
jpayne@69:     my $err = "ERROR: Failed to run nucmer, aborting.\n";
jpayne@69: 
jpayne@69:     system($cmd) == 0 or die $err;
jpayne@69:     $OPT_DeltaFile = $OPT_Prefix . ".delta";
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #---------------------------------------------------------------- RunFilter ----
jpayne@69: # Run delta-filter
jpayne@69: sub RunFilter()
jpayne@69: {
jpayne@69:     print STDERR "Filtering alignments\n";
jpayne@69:     my $cmd1 = "$DELTA_FILTER -1 $OPT_DeltaFile > $OPT_DeltaFile1";
jpayne@69:     my $cmd2 = "$DELTA_FILTER -m $OPT_DeltaFile > $OPT_DeltaFileM";
jpayne@69:     my $err = "ERROR: Failed to run delta-filter, aborting.\n";
jpayne@69: 
jpayne@69:     system($cmd1) == 0 or die $err;
jpayne@69:     system($cmd2) == 0 or die $err;
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #------------------------------------------------------------------ RunSNPs ----
jpayne@69: # Run show-snps
jpayne@69: sub RunSNPs()
jpayne@69: {
jpayne@69:     print STDERR "Analyzing SNPs\n";
jpayne@69:     my $cmd = "$SHOW_SNPS -rlTHC $OPT_DeltaFile1 > $OPT_SnpsFile";
jpayne@69:     my $err = "ERROR: Failed to run show-snps, aborting.\n";
jpayne@69: 
jpayne@69:     system($cmd) == 0 or die $err;
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #---------------------------------------------------------------- RunCoords ----
jpayne@69: # Run show-coords
jpayne@69: sub RunCoords()
jpayne@69: {
jpayne@69:     print STDERR "Extracting alignment coordinates\n";
jpayne@69:     my $cmd1 = "$SHOW_COORDS -rclTH $OPT_DeltaFile1 > $OPT_CoordsFile1";
jpayne@69:     my $cmd2 = "$SHOW_COORDS -rclTH $OPT_DeltaFileM > $OPT_CoordsFileM";
jpayne@69:     my $err = "ERROR: Failed to run show-coords, aborting.\n";
jpayne@69: 
jpayne@69:     system($cmd1) == 0 or die $err;
jpayne@69:     system($cmd2) == 0 or die $err;
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #------------------------------------------------------------------ RunDiff ----
jpayne@69: # Run show-diff
jpayne@69: sub RunDiff()
jpayne@69: {
jpayne@69:     print STDERR "Extracting alignment breakpoints\n";
jpayne@69:     my $cmd1 = "$SHOW_DIFF -rH $OPT_DeltaFileM > $OPT_DiffRFile";
jpayne@69:     my $cmd2 = "$SHOW_DIFF -qH $OPT_DeltaFileM > $OPT_DiffQFile";
jpayne@69:     my $err = "ERROR: Failed to run show-diff, aborting.\n";
jpayne@69: 
jpayne@69:     system($cmd1) == 0 or die $err;
jpayne@69:     system($cmd2) == 0 or die $err;
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #--------------------------------------------------------------- MakeReport ----
jpayne@69: # Output alignment report
jpayne@69: sub MakeReport()
jpayne@69: {
jpayne@69:     print STDERR "Generating report file\n";
jpayne@69: 
jpayne@69:     my ($fhi, $fho);    # filehandle-in and filehandle-out
jpayne@69:     my (%refs, %qrys) = ((),());            # R and Q ID->length
jpayne@69:     my ($rqnAligns1, $rqnAlignsM) = (0,0);  # alignment counter
jpayne@69:     my ($rSumLen1, $qSumLen1) = (0,0);      # alignment length sum
jpayne@69:     my ($rSumLenM, $qSumLenM) = (0,0);      # alignment length sum
jpayne@69:     my ($rqSumLen1, $rqSumLenM) = (0,0);    # combined alignment length sum
jpayne@69:     my ($rqSumIdy1, $rqSumIdyM) = (0,0);    # weighted alignment identity sum
jpayne@69:     my ($qnIns, $rnIns) = (0,0);            # insertion count
jpayne@69:     my ($qSumIns, $rSumIns) = (0,0);        # insertion length sum
jpayne@69:     my ($qnTIns, $rnTIns) = (0,0);          # tandem insertion count
jpayne@69:     my ($qSumTIns, $rSumTIns) = (0,0);      # tandem insertion length sum
jpayne@69:     my ($qnInv, $rnInv) = (0,0);            # inversion count
jpayne@69:     my ($qnRel, $rnRel) = (0,0);            # relocation count
jpayne@69:     my ($qnTrn, $rnTrn) = (0,0);            # translocation count
jpayne@69:     my ($rnSeqs, $qnSeqs) = (0,0);          # sequence count
jpayne@69:     my ($rnASeqs, $qnASeqs) = (0,0);        # aligned sequence count
jpayne@69:     my ($rnBases, $qnBases) = (0,0);        # bases count
jpayne@69:     my ($rnABases, $qnABases) = (0,0);      # aligned bases count
jpayne@69:     my ($rnBrk, $qnBrk) = (0,0);            # breakpoint count
jpayne@69:     my ($rqnSNPs, $rqnIndels) = (0,0);      # snp and indel counts
jpayne@69:     my ($rqnGSNPs, $rqnGIndels) = (0,0);    # good snp and indel counts
jpayne@69:     my %rqSNPs =                            # SNP hash
jpayne@69:       ( "."=>{"A"=>0,"C"=>0,"G"=>0,"T"=>0},
jpayne@69:         "A"=>{"."=>0,"C"=>0,"G"=>0,"T"=>0},
jpayne@69:         "C"=>{"."=>0,"A"=>0,"G"=>0,"T"=>0},
jpayne@69:         "G"=>{"."=>0,"A"=>0,"C"=>0,"T"=>0},
jpayne@69:         "T"=>{"."=>0,"A"=>0,"C"=>0,"G"=>0} );
jpayne@69:     my %rqGSNPs =                           # good SNP hash
jpayne@69:       ( "."=>{"A"=>0,"C"=>0,"G"=>0,"T"=>0},
jpayne@69:         "A"=>{"."=>0,"C"=>0,"G"=>0,"T"=>0},
jpayne@69:         "C"=>{"."=>0,"A"=>0,"G"=>0,"T"=>0},
jpayne@69:         "G"=>{"."=>0,"A"=>0,"C"=>0,"T"=>0},
jpayne@69:         "T"=>{"."=>0,"A"=>0,"C"=>0,"G"=>0} );
jpayne@69: 
jpayne@69:     my $header;                             # delta header
jpayne@69: 
jpayne@69:     #-- Get delta header
jpayne@69:     $fhi = FileOpen("<", $OPT_DeltaFile);
jpayne@69:     $header .= <$fhi>;
jpayne@69:     $header .= <$fhi>;
jpayne@69:     $header .= "\n";
jpayne@69:     FileClose($fhi, $OPT_DeltaFile);
jpayne@69: 
jpayne@69:     #-- Collect all reference and query IDs and lengths
jpayne@69:     FastaSizes($OPT_RefFile, \%refs);
jpayne@69:     FastaSizes($OPT_QryFile, \%qrys);
jpayne@69: 
jpayne@69:     #-- Count ref and qry seqs and lengths
jpayne@69:     foreach ( values(%refs) ) {
jpayne@69:         $rnSeqs++;
jpayne@69:         $rnBases += $_;
jpayne@69:     }
jpayne@69:     foreach ( values(%qrys) ) {
jpayne@69:         $qnSeqs++;
jpayne@69:         $qnBases += $_;
jpayne@69:     }
jpayne@69: 
jpayne@69:     #-- Count aligned seqs, aligned bases, and breakpoints for each R and Q
jpayne@69:     $fhi = FileOpen("<", $OPT_CoordsFileM);
jpayne@69:     while (<$fhi>) {
jpayne@69:         chomp;
jpayne@69:         my @A = split "\t";
jpayne@69:         scalar(@A) == 13
jpayne@69:             or die "ERROR: Unrecognized format $OPT_CoordsFileM, aborting.\n";
jpayne@69: 
jpayne@69:         #-- Add to M-to-M alignment counts
jpayne@69:         $rqnAlignsM++;
jpayne@69:         $rSumLenM += $A[4];
jpayne@69:         $qSumLenM += $A[5];
jpayne@69:         $rqSumIdyM += ($A[6] / 100.0) * ($A[4] + $A[5]);
jpayne@69:         $rqSumLenM += ($A[4] + $A[5]);
jpayne@69: 
jpayne@69:         #-- If new ID, add to sequence and base count
jpayne@69:         if ( $refs{$A[11]} > 0 ) {
jpayne@69:             $rnASeqs++;
jpayne@69:             $rnABases += $refs{$A[11]};
jpayne@69:             $refs{$A[11]} *= -1; # If ref has alignment, length will be -neg
jpayne@69:         }
jpayne@69:         if ( $qrys{$A[12]} > 0 ) {
jpayne@69:             $qnASeqs++;
jpayne@69:             $qnABases += $qrys{$A[12]};
jpayne@69:             $qrys{$A[12]} *= -1; # If qry has alignment, length will be -neg
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Add to breakpoint counts
jpayne@69:         my ($lo, $hi);
jpayne@69:         if ( $A[0] < $A[1] ) { $lo = $A[0]; $hi = $A[1]; }
jpayne@69:         else                 { $lo = $A[1]; $hi = $A[0]; }
jpayne@69:         $rnBrk++ if ( $lo != 1 );
jpayne@69:         $rnBrk++ if ( $hi != $A[7] );
jpayne@69: 
jpayne@69:         if ( $A[2] < $A[3] ) { $lo = $A[2]; $hi = $A[3]; }
jpayne@69:         else                 { $lo = $A[3]; $hi = $A[2]; }
jpayne@69:         $qnBrk++ if ( $lo != 1 );
jpayne@69:         $qnBrk++ if ( $hi != $A[8] );
jpayne@69:     }
jpayne@69:     FileClose($fhi, $OPT_CoordsFileM);
jpayne@69: 
jpayne@69:     #-- Calculate average %idy, length, etc.
jpayne@69:     $fhi = FileOpen("<", $OPT_CoordsFile1);
jpayne@69:     while (<$fhi>) {
jpayne@69:         chomp;
jpayne@69:         my @A = split "\t";
jpayne@69:         scalar(@A) == 13
jpayne@69:             or die "ERROR: Unrecognized format $OPT_CoordsFile1, aborting.\n";
jpayne@69: 
jpayne@69:         #-- Add to 1-to-1 alignment counts
jpayne@69:         $rqnAligns1++;
jpayne@69:         $rSumLen1 += $A[4];
jpayne@69:         $qSumLen1 += $A[5];
jpayne@69:         $rqSumIdy1 += ($A[6] / 100.0) * ($A[4] + $A[5]);
jpayne@69:         $rqSumLen1 += ($A[4] + $A[5]);
jpayne@69:     }
jpayne@69:     FileClose($fhi, $OPT_CoordsFile1);
jpayne@69: 
jpayne@69:     #-- If you are reading this, you need to get out more...
jpayne@69: 
jpayne@69:     #-- Count reference diff features and indels
jpayne@69:     $fhi = FileOpen("<", $OPT_DiffRFile);
jpayne@69:     while (<$fhi>) {
jpayne@69:         chomp;
jpayne@69:         my @A = split "\t";
jpayne@69:         defined($A[4])
jpayne@69:             or die "ERROR: Unrecognized format $OPT_DiffRFile, aborting.\n";
jpayne@69:         my $gap = $A[4];
jpayne@69:         my $ins = $gap;
jpayne@69: 
jpayne@69:         #-- Add to tandem insertion counts
jpayne@69:         if ( $A[1] eq "GAP" ) {
jpayne@69:             scalar(@A) == 7
jpayne@69:                 or die "ERROR: Unrecognized format $OPT_DiffRFile, aborting.\n";
jpayne@69:             $ins = $A[6] if ( $A[6] > $gap );
jpayne@69:             if ( $A[4] <= 0 && $A[5] <= 0 && $A[6] > 0 ) {
jpayne@69:                 $rnTIns++;
jpayne@69:                 $rSumTIns += $A[6];
jpayne@69:              }
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Remove unaligned sequence from count
jpayne@69:         if ( $A[1] ne "DUP" ) {
jpayne@69:           $rnABases -= $gap if ( $gap > 0 );
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Add to insertion count
jpayne@69:         if ( $ins > 0 ) {
jpayne@69:             $rnIns++;
jpayne@69:             $rSumIns += $ins;
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Add to rearrangement counts
jpayne@69:         $rnInv++ if ( $A[1] eq "INV" );
jpayne@69:         $rnRel++ if ( $A[1] eq "JMP" );
jpayne@69:         $rnTrn++ if ( $A[1] eq "SEQ" );
jpayne@69:     }
jpayne@69:     FileClose($fhi, $OPT_DiffRFile);
jpayne@69: 
jpayne@69:     #-- Count query diff features and indels
jpayne@69:     $fhi = FileOpen("<", $OPT_DiffQFile);
jpayne@69:     while (<$fhi>) {
jpayne@69:         chomp;
jpayne@69:         my @A = split "\t";
jpayne@69:         defined($A[4])
jpayne@69:             or die "ERROR: Unrecognized format $OPT_DiffRFile, aborting.\n";
jpayne@69:         my $gap = $A[4];
jpayne@69:         my $ins = $gap;
jpayne@69: 
jpayne@69:         #-- Add to tandem insertion counts
jpayne@69:         if ( $A[1] eq "GAP" ) {
jpayne@69:             scalar(@A) == 7
jpayne@69:                 or die "ERROR: Unrecognized format $OPT_DiffRFile, aborting.\n";
jpayne@69:             $ins = $A[6] if ( $A[6] > $gap );
jpayne@69:             if ( $A[4] <= 0 && $A[5] <= 0 && $A[6] > 0 ) {
jpayne@69:                 $qnTIns++;
jpayne@69:                 $qSumTIns += $A[6];
jpayne@69:             }
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Remove unaligned sequence from count
jpayne@69:         if ( $A[1] ne "DUP" ) {
jpayne@69:           $qnABases -= $gap if ( $gap > 0 );
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Add to insertion count
jpayne@69:         if ( $ins > 0 ) {
jpayne@69:             $qnIns++;
jpayne@69:             $qSumIns += $ins;
jpayne@69:         }
jpayne@69: 
jpayne@69:         #-- Add to rearrangement counts
jpayne@69:         $qnInv++ if ( $A[1] eq "INV" );
jpayne@69:         $qnRel++ if ( $A[1] eq "JMP" );
jpayne@69:         $qnTrn++ if ( $A[1] eq "SEQ" );
jpayne@69:     }
jpayne@69:     FileClose($fhi, $OPT_DiffQFile);
jpayne@69: 
jpayne@69:     #-- Count SNPs
jpayne@69:     $fhi = FileOpen("<", $OPT_SnpsFile);
jpayne@69:     while(<$fhi>) {
jpayne@69:         chomp;
jpayne@69:         my @A = split "\t";
jpayne@69:         scalar(@A) == 12
jpayne@69:             or die "ERROR: Unrecognized format $OPT_SnpsFile, aborting\n";
jpayne@69: 
jpayne@69:         my $r = uc($A[1]);
jpayne@69:         my $q = uc($A[2]);
jpayne@69: 
jpayne@69:         #-- Plain SNPs
jpayne@69:         $rqSNPs{$r}{$q}++;
jpayne@69:         if ( !exists($rqSNPs{$q}{$r}) ) { $rqSNPs{$q}{$r} = 0; }
jpayne@69:         if ( $r eq '.' || $q eq '.' ) { $rqnIndels++; }
jpayne@69:         else                          { $rqnSNPs++; }
jpayne@69: 
jpayne@69:         #-- Good SNPs with sufficient match buffer
jpayne@69:         if ( $A[4] >= $SNPBuff ) {
jpayne@69:             $rqGSNPs{$r}{$q}++;
jpayne@69:             if ( !exists($rqGSNPs{$q}{$r}) ) { $rqGSNPs{$q}{$r} = 0; }
jpayne@69:             if ( $r eq '.' || $q eq '.' ) { $rqnGIndels++; }
jpayne@69:             else                          { $rqnGSNPs++; }
jpayne@69:         }
jpayne@69:     }
jpayne@69:     FileClose($fhi, $OPT_SnpsFile);
jpayne@69: 
jpayne@69: 
jpayne@69:     #-- Output report
jpayne@69:     $fho = FileOpen(">", $OPT_ReportFile);
jpayne@69: 
jpayne@69:     print  $fho $header;
jpayne@69:     printf $fho "%-15s %20s %20s\n", "", "[REF]", "[QRY]";
jpayne@69: 
jpayne@69:     print  $fho "[Sequences]\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalSeqs", $rnSeqs, $qnSeqs;
jpayne@69:     printf $fho "%-15s %20s %20s\n",
jpayne@69:     "AlignedSeqs",
jpayne@69:     ( sprintf "%10d(%.2f%%)",
jpayne@69:       $rnASeqs, ($rnSeqs ? $rnASeqs / $rnSeqs * 100.0 : 0) ),
jpayne@69:     ( sprintf "%10d(%.2f%%)",
jpayne@69:       $qnASeqs, ($rnSeqs ? $qnASeqs / $qnSeqs * 100.0 : 0) );
jpayne@69:     printf $fho "%-15s %20s %20s\n",
jpayne@69:     "UnalignedSeqs",
jpayne@69:      ( sprintf "%10d(%.2f%%)",
jpayne@69:        $rnSeqs - $rnASeqs,
jpayne@69:        ($rnSeqs ? ($rnSeqs - $rnASeqs) / $rnSeqs * 100.0 : 0) ),
jpayne@69:      ( sprintf "%10d(%.2f%%)",
jpayne@69:        $qnSeqs - $qnASeqs,
jpayne@69:        ($qnSeqs ? ($qnSeqs - $qnASeqs) / $qnSeqs * 100.0 : 0) );
jpayne@69: 
jpayne@69:     print  $fho "\n[Bases]\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalBases", $rnBases, $qnBases;
jpayne@69:     printf $fho "%-15s %20s %20s\n",
jpayne@69:     "AlignedBases",
jpayne@69:     ( sprintf "%10d(%.2f%%)",
jpayne@69:       $rnABases, ($rnBases ? $rnABases / $rnBases * 100.0 : 0) ),
jpayne@69:     ( sprintf "%10d(%.2f%%)",
jpayne@69:       $qnABases, ($qnBases ? $qnABases / $qnBases * 100.0 : 0) );
jpayne@69:     printf $fho "%-15s %20s %20s\n",
jpayne@69:     "UnalignedBases",
jpayne@69:     ( sprintf "%10d(%.2f%%)",
jpayne@69:       $rnBases - $rnABases,
jpayne@69:       ($rnBases ? ($rnBases - $rnABases) / $rnBases * 100.0 : 0) ),
jpayne@69:     ( sprintf "%10d(%.2f%%)",
jpayne@69:       $qnBases - $qnABases,
jpayne@69:       ($qnBases ? ($qnBases - $qnABases) / $qnBases * 100.0 : 0) );
jpayne@69: 
jpayne@69:     print  $fho "\n[Alignments]\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "1-to-1", $rqnAligns1, $rqnAligns1;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalLength", $rSumLen1, $qSumLen1;
jpayne@69:     printf $fho "%-15s %20.2f %20.2f\n",
jpayne@69:     "AvgLength",
jpayne@69:     ($rqnAligns1 ? $rSumLen1 / $rqnAligns1 : 0),
jpayne@69:     ($rqnAligns1 ? $qSumLen1 / $rqnAligns1 : 0);
jpayne@69:     printf $fho "%-15s %20.2f %20.2f\n",
jpayne@69:     "AvgIdentity",
jpayne@69:     ($rqSumLen1 ? $rqSumIdy1 / $rqSumLen1 * 100.0 : 0),
jpayne@69:     ($rqSumLen1 ? $rqSumIdy1 / $rqSumLen1 * 100.0 : 0);
jpayne@69: 
jpayne@69:     print  $fho "\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "M-to-M", $rqnAlignsM, $rqnAlignsM;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalLength", $rSumLenM, $qSumLenM;
jpayne@69:     printf $fho "%-15s %20.2f %20.2f\n",
jpayne@69:     "AvgLength",
jpayne@69:     ($rqnAlignsM ? $rSumLenM / $rqnAlignsM : 0),
jpayne@69:     ($rqnAlignsM ? $qSumLenM / $rqnAlignsM : 0);
jpayne@69:     printf $fho "%-15s %20.2f %20.2f\n",
jpayne@69:     "AvgIdentity",
jpayne@69:     ($rqSumLenM ? $rqSumIdyM / $rqSumLenM * 100.0 : 0),
jpayne@69:     ($rqSumLenM ? $rqSumIdyM / $rqSumLenM * 100.0 : 0);
jpayne@69: 
jpayne@69:     print  $fho "\n[Feature Estimates]\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "Breakpoints", $rnBrk, $qnBrk;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "Relocations", $rnRel, $qnRel;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "Translocations", $rnTrn, $qnTrn;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "Inversions", $rnInv, $qnInv;
jpayne@69: 
jpayne@69:     print  $fho "\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "Insertions", $rnIns, $qnIns;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "InsertionSum", $rSumIns, $qSumIns;
jpayne@69:     printf $fho "%-15s %20.2f %20.2f\n",
jpayne@69:     "InsertionAvg",
jpayne@69:     ($rnIns ? $rSumIns / $rnIns : 0),
jpayne@69:     ($qnIns ? $qSumIns / $qnIns : 0);
jpayne@69: 
jpayne@69:     print  $fho "\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TandemIns", $rnTIns, $qnTIns;
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TandemInsSum", $rSumTIns, $qSumTIns;
jpayne@69:     printf $fho "%-15s %20.2f %20.2f\n",
jpayne@69:     "TandemInsAvg",
jpayne@69:     ($rnTIns ? $rSumTIns / $rnTIns : 0),
jpayne@69:     ($qnTIns ? $qSumTIns / $qnTIns : 0);
jpayne@69: 
jpayne@69:     print  $fho "\n[SNPs]\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalSNPs", $rqnSNPs, $rqnSNPs;
jpayne@69:     foreach my $r (keys %rqSNPs) {
jpayne@69:       foreach my $q (keys %{$rqSNPs{$r}}) {
jpayne@69:         if ( $r ne "." && $q ne "." ) {
jpayne@69:           printf $fho "%-15s %20s %20s\n",
jpayne@69:             "$r$q",
jpayne@69:               ( sprintf "%10d(%.2f%%)",
jpayne@69:                 $rqSNPs{$r}{$q},
jpayne@69:                 ($rqnSNPs ? $rqSNPs{$r}{$q} / $rqnSNPs * 100.0 : 0) ),
jpayne@69:                   ( sprintf "%10d(%.2f%%)",
jpayne@69:                     $rqSNPs{$q}{$r},
jpayne@69:                     ($rqnSNPs ? $rqSNPs{$q}{$r} / $rqnSNPs * 100.0 : 0) );
jpayne@69:         }
jpayne@69:       }
jpayne@69:     }
jpayne@69: 
jpayne@69:     print  $fho "\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalGSNPs", $rqnGSNPs, $rqnGSNPs;
jpayne@69:     foreach my $r (keys %rqGSNPs) {
jpayne@69:       foreach my $q (keys %{$rqGSNPs{$r}}) {
jpayne@69:         if ( $r ne "." && $q ne "." ) {
jpayne@69:           printf $fho "%-15s %20s %20s\n",
jpayne@69:             "$r$q",
jpayne@69:               ( sprintf "%10d(%.2f%%)",
jpayne@69:                 $rqGSNPs{$r}{$q},
jpayne@69:                 ($rqnGSNPs ? $rqGSNPs{$r}{$q} / $rqnGSNPs * 100.0 : 0) ),
jpayne@69:                   ( sprintf "%10d(%.2f%%)",
jpayne@69:                     $rqGSNPs{$q}{$r},
jpayne@69:                     ($rqnGSNPs ? $rqGSNPs{$q}{$r} / $rqnGSNPs * 100.0 : 0) );
jpayne@69:         }
jpayne@69:       }
jpayne@69:     }
jpayne@69: 
jpayne@69:     print  $fho "\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalIndels", $rqnIndels, $rqnIndels;
jpayne@69:     foreach my $r (keys %rqSNPs) {
jpayne@69:       foreach my $q (keys %{$rqSNPs{$r}}) {
jpayne@69:         if ( $q eq "." ) {
jpayne@69:           printf $fho "%-15s %20s %20s\n",
jpayne@69:             "$r$q",
jpayne@69:               ( sprintf "%10d(%.2f%%)",
jpayne@69:                 $rqSNPs{$r}{$q},
jpayne@69:                 ($rqnIndels ? $rqSNPs{$r}{$q} / $rqnIndels * 100.0 : 0) ),
jpayne@69:                   ( sprintf "%10d(%.2f%%)",
jpayne@69:                     $rqSNPs{$q}{$r},
jpayne@69:                     ($rqnIndels ? $rqSNPs{$q}{$r} / $rqnIndels * 100.0 : 0) );
jpayne@69:         }
jpayne@69:       }
jpayne@69:     }
jpayne@69:     foreach my $r (keys %rqSNPs) {
jpayne@69:       foreach my $q (keys %{$rqSNPs{$r}}) {
jpayne@69:         if ( $r eq "." ) {
jpayne@69:           printf $fho "%-15s %20s %20s\n",
jpayne@69:             "$r$q",
jpayne@69:               ( sprintf "%10d(%.2f%%)",
jpayne@69:                 $rqSNPs{$r}{$q},
jpayne@69:                 ($rqnIndels ? $rqSNPs{$r}{$q} / $rqnIndels * 100.0 : 0) ),
jpayne@69:                   ( sprintf "%10d(%.2f%%)",
jpayne@69:                     $rqSNPs{$q}{$r},
jpayne@69:                     ($rqnIndels ? $rqSNPs{$q}{$r} / $rqnIndels * 100.0 : 0) );
jpayne@69:         }
jpayne@69:       }
jpayne@69:     }
jpayne@69: 
jpayne@69:     print  $fho "\n";
jpayne@69: 
jpayne@69:     printf $fho "%-15s %20d %20d\n",
jpayne@69:     "TotalGIndels", $rqnGIndels, $rqnGIndels;
jpayne@69:     foreach my $r (keys %rqGSNPs) {
jpayne@69:       foreach my $q (keys %{$rqGSNPs{$r}}) {
jpayne@69:         if ( $q eq "." ) {
jpayne@69:           printf $fho "%-15s %20s %20s\n",
jpayne@69:             "$r$q",
jpayne@69:               ( sprintf "%10d(%.2f%%)",
jpayne@69:                 $rqGSNPs{$r}{$q},
jpayne@69:                 ($rqnGIndels ? $rqGSNPs{$r}{$q} / $rqnGIndels * 100.0 : 0) ),
jpayne@69:                   ( sprintf "%10d(%.2f%%)",
jpayne@69:                     $rqGSNPs{$q}{$r},
jpayne@69:                     ($rqnGIndels ? $rqGSNPs{$q}{$r} / $rqnGIndels * 100.0 : 0) );
jpayne@69:         }
jpayne@69:       }
jpayne@69:     }
jpayne@69:     foreach my $r (keys %rqGSNPs) {
jpayne@69:       foreach my $q (keys %{$rqGSNPs{$r}}) {
jpayne@69:         if ( $r eq "." ) {
jpayne@69:           printf $fho "%-15s %20s %20s\n",
jpayne@69:             "$r$q",
jpayne@69:               ( sprintf "%10d(%.2f%%)",
jpayne@69:                 $rqGSNPs{$r}{$q},
jpayne@69:                 ($rqnGIndels ? $rqGSNPs{$r}{$q} / $rqnGIndels * 100.0 : 0) ),
jpayne@69:                   ( sprintf "%10d(%.2f%%)",
jpayne@69:                     $rqGSNPs{$q}{$r},
jpayne@69:                     ($rqnGIndels ? $rqGSNPs{$q}{$r} / $rqnGIndels * 100.0 : 0) );
jpayne@69:         }
jpayne@69:       }
jpayne@69:     }
jpayne@69: 
jpayne@69:     FileClose($fho, $OPT_ReportFile);
jpayne@69: 
jpayne@69: 
jpayne@69:     #-- Output unaligned reference and query IDs, if applicable
jpayne@69:     if ( $rnSeqs != $rnASeqs ) {
jpayne@69:         $fho = FileOpen(">", $OPT_UnRefFile);
jpayne@69:         while ( my ($key, $val) = each(%refs) ) {
jpayne@69:             print $fho "$key\tUNI\t1\t$val\t$val\n" unless $val < 0;
jpayne@69:         }
jpayne@69:         FileClose($fho, $OPT_UnRefFile);
jpayne@69:     }
jpayne@69:     if ( $qnSeqs != $qnASeqs ) {
jpayne@69:         $fho = FileOpen(">", $OPT_UnQryFile);
jpayne@69:         while ( my ($key, $val) = each(%qrys) ) {
jpayne@69:             print $fho "$key\tUNI\t1\t$val\t$val\n" unless $val < 0;
jpayne@69:         }
jpayne@69:         FileClose($fho, $OPT_UnQryFile);
jpayne@69:     }
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #--------------------------------------------------------------- FastaSizes ----
jpayne@69: # Compute lengths for a multi-fasta file and store in hash reference
jpayne@69: sub FastaSizes($$)
jpayne@69: {
jpayne@69: 
jpayne@69:     my $file = shift;
jpayne@69:     my $href = shift;
jpayne@69:     my ($tag, $len);
jpayne@69: 
jpayne@69:     my $fhi = FileOpen("<", $file);
jpayne@69:     while (<$fhi>) {
jpayne@69:         chomp;
jpayne@69: 
jpayne@69:         if ( /^>/ ) {
jpayne@69:             $href->{$tag} = $len if defined($tag);
jpayne@69:             ($tag) = /^>(\S+)/;
jpayne@69:             $len = 0;
jpayne@69:         } else {
jpayne@69:             if ( /\s/ ) {
jpayne@69:                 die "ERROR: Whitespace found in FastA $file, aborting.\n";
jpayne@69:             }
jpayne@69:             $len += length;
jpayne@69:         }
jpayne@69:     }
jpayne@69:     $href->{$tag} = $len if defined($tag);
jpayne@69:     FileClose($fhi, $file);
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #----------------------------------------------------------------- FileOpen ----
jpayne@69: # Open file, return filehandle, or die
jpayne@69: sub FileOpen($$)
jpayne@69: {
jpayne@69:     my ($mode, $name) = @_;
jpayne@69:     my $fhi;
jpayne@69:     open($fhi, $mode, $name)
jpayne@69:         or die "ERROR: Could not open $name, aborting. $!\n";
jpayne@69:     return $fhi;
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #---------------------------------------------------------------- FileClose ----
jpayne@69: # Close file, or die
jpayne@69: sub FileClose($$)
jpayne@69: {
jpayne@69:     my ($fho, $name) = @_;
jpayne@69:     close($fho) or die "ERROR: Could not close $name, aborting. $!\n"
jpayne@69: }
jpayne@69: 
jpayne@69: 
jpayne@69: #------------------------------------------------------------------- GetOpt ----
jpayne@69: # Get command options and check file permissions
jpayne@69: sub GetOpt()
jpayne@69: {
jpayne@69:     #-- Initialize TIGR::Foundation
jpayne@69:     $TIGR = new TIGR::Foundation;
jpayne@69:     if ( !defined($TIGR) ) {
jpayne@69:         print STDERR "ERROR: TIGR::Foundation could not be initialized";
jpayne@69:         exit(1);
jpayne@69:     }
jpayne@69: 
jpayne@69:     #-- Set help and usage information
jpayne@69:     $TIGR->setHelpInfo($HELP_INFO);
jpayne@69:     $TIGR->setUsageInfo($USAGE_INFO);
jpayne@69:     $TIGR->setVersionInfo($VERSION_INFO);
jpayne@69:     $TIGR->addDependInfo(@DEPEND_INFO);
jpayne@69: 
jpayne@69:     #-- Get options
jpayne@69:     my $err = !$TIGR->TIGR_GetOptions
jpayne@69:         (
jpayne@69:          "d|delta=s"  => \$OPT_DeltaFile,
jpayne@69:          "p|prefix=s" => \$OPT_Prefix,
jpayne@69:          );
jpayne@69: 
jpayne@69:     #-- Check if the parsing was successful
jpayne@69:     if ( $err
jpayne@69:          || (defined($OPT_DeltaFile) && scalar(@ARGV) != 0)
jpayne@69:          || (!defined($OPT_DeltaFile) && scalar(@ARGV) != 2) ) {
jpayne@69:         $TIGR->printUsageInfo();
jpayne@69:         print STDERR "Try '$0 -h' for more information.\n";
jpayne@69:         exit(1);
jpayne@69:     }
jpayne@69: 
jpayne@69:     my @errs;
jpayne@69: 
jpayne@69:     $TIGR->isExecutableFile($DELTA_FILTER)
jpayne@69:         or push(@errs, $DELTA_FILTER);
jpayne@69: 
jpayne@69:     $TIGR->isExecutableFile($SHOW_DIFF)
jpayne@69:         or push(@errs, $SHOW_DIFF);
jpayne@69: 
jpayne@69:     $TIGR->isExecutableFile($SHOW_SNPS)
jpayne@69:         or push(@errs, $SHOW_SNPS);
jpayne@69: 
jpayne@69:     $TIGR->isExecutableFile($SHOW_COORDS)
jpayne@69:         or push(@errs, $SHOW_COORDS);
jpayne@69: 
jpayne@69:     $TIGR->isExecutableFile($NUCMER)
jpayne@69:         or push(@errs, $NUCMER);
jpayne@69: 
jpayne@69:     if ( defined($OPT_DeltaFile) ) {
jpayne@69:         $TIGR->isReadableFile($OPT_DeltaFile)
jpayne@69:             or push(@errs, $OPT_DeltaFile);
jpayne@69: 
jpayne@69:         my $fhi = FileOpen("<", $OPT_DeltaFile);
jpayne@69:         $_ = <$fhi>;
jpayne@69:         FileClose($fhi, $OPT_DeltaFile);
jpayne@69: 
jpayne@69:         ($OPT_RefFile, $OPT_QryFile) = /^(.+) (.+)$/;
jpayne@69:     }
jpayne@69:     else {
jpayne@69:         $OPT_RefFile = File::Spec->rel2abs($ARGV[0]);
jpayne@69:         $OPT_QryFile = File::Spec->rel2abs($ARGV[1]);
jpayne@69:     }
jpayne@69: 
jpayne@69:     $TIGR->isReadableFile($OPT_RefFile)
jpayne@69:         or push(@errs, $OPT_RefFile);
jpayne@69: 
jpayne@69:     $TIGR->isReadableFile($OPT_QryFile)
jpayne@69:         or push(@errs, $OPT_QryFile);
jpayne@69: 
jpayne@69:     $OPT_ReportFile = $OPT_Prefix . $OPT_ReportFile;
jpayne@69:     $TIGR->isCreatableFile("$OPT_ReportFile")
jpayne@69:         or $TIGR->isWritableFile("$OPT_ReportFile")
jpayne@69:         or push(@errs, "$OPT_ReportFile");
jpayne@69: 
jpayne@69:     $OPT_DeltaFile1 = $OPT_Prefix . $OPT_DeltaFile1;
jpayne@69:     $TIGR->isCreatableFile("$OPT_DeltaFile1")
jpayne@69:         or $TIGR->isWritableFile("$OPT_DeltaFile1")
jpayne@69:         or push(@errs, "$OPT_DeltaFile1");
jpayne@69: 
jpayne@69:     $OPT_DeltaFileM = $OPT_Prefix . $OPT_DeltaFileM;
jpayne@69:     $TIGR->isCreatableFile("$OPT_DeltaFileM")
jpayne@69:         or $TIGR->isWritableFile("$OPT_DeltaFileM")
jpayne@69:         or push(@errs, "$OPT_DeltaFileM");
jpayne@69: 
jpayne@69:     $OPT_CoordsFile1 = $OPT_Prefix . $OPT_CoordsFile1;
jpayne@69:     $TIGR->isCreatableFile("$OPT_CoordsFile1")
jpayne@69:         or $TIGR->isWritableFile("$OPT_CoordsFile1")
jpayne@69:         or push(@errs, "$OPT_CoordsFile1");
jpayne@69: 
jpayne@69:     $OPT_CoordsFileM = $OPT_Prefix . $OPT_CoordsFileM;
jpayne@69:     $TIGR->isCreatableFile("$OPT_CoordsFileM")
jpayne@69:         or $TIGR->isWritableFile("$OPT_CoordsFileM")
jpayne@69:         or push(@errs, "$OPT_CoordsFileM");
jpayne@69: 
jpayne@69:     $OPT_SnpsFile = $OPT_Prefix . $OPT_SnpsFile;
jpayne@69:     $TIGR->isCreatableFile("$OPT_SnpsFile")
jpayne@69:         or $TIGR->isWritableFile("$OPT_SnpsFile")
jpayne@69:         or push(@errs, "$OPT_SnpsFile");
jpayne@69: 
jpayne@69:     $OPT_DiffRFile = $OPT_Prefix . $OPT_DiffRFile;
jpayne@69:     $TIGR->isCreatableFile("$OPT_DiffRFile")
jpayne@69:         or $TIGR->isWritableFile("$OPT_DiffRFile")
jpayne@69:         or push(@errs, "$OPT_DiffRFile");
jpayne@69: 
jpayne@69:     $OPT_DiffQFile = $OPT_Prefix . $OPT_DiffQFile;
jpayne@69:     $TIGR->isCreatableFile("$OPT_DiffQFile")
jpayne@69:         or $TIGR->isWritableFile("$OPT_DiffQFile")
jpayne@69:         or push(@errs, "$OPT_DiffQFile");
jpayne@69: 
jpayne@69:     $OPT_UnRefFile = $OPT_Prefix . $OPT_UnRefFile;
jpayne@69:         $TIGR->isCreatableFile("$OPT_UnRefFile")
jpayne@69:         or $TIGR->isWritableFile("$OPT_UnRefFile")
jpayne@69:         or push(@errs, "$OPT_UnRefFile");
jpayne@69: 
jpayne@69:     $OPT_UnQryFile = $OPT_Prefix . $OPT_UnQryFile;
jpayne@69:         $TIGR->isCreatableFile("$OPT_UnQryFile")
jpayne@69:         or $TIGR->isWritableFile("$OPT_UnQryFile")
jpayne@69:         or push(@errs, "$OPT_UnQryFile");
jpayne@69: 
jpayne@69:     if ( scalar(@errs) ) {
jpayne@69:         print STDERR "ERROR: The following critical files could not be used\n";
jpayne@69:         while ( scalar(@errs) ) { print(STDERR pop(@errs),"\n"); }
jpayne@69:         print STDERR "Check your paths and file permissions and try again\n";
jpayne@69:         exit(1);
jpayne@69:     }
jpayne@69: }