genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 46)

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Update of /cvsroot/genex/genex-server/DB/scripts
In directory usw-pr-cvs1:/tmp/cvs-serv23975/DB/scripts

Added Files:
	fix-array.pl tab2AD.pl 
Log Message:
new


--- NEW FILE: fix-array.pl ---
#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;

my %OPTIONS;
my $rc = GetOptions(\%OPTIONS,
		    'mangle',
		    'infile=s',
		    'outfile=s',
		    'design=s',
		    'help',
		   );

my $USAGE = <<"EOU";
usage: $0 [required flags] file1 ...
  required flags:
    --infile=file     : the file to read

  optional flags:
    --outfile=file    : the (adjusted) file to write
    --design=file     : the array design file to create
    --help            : print this message
EOU

die "Bad option\n$USAGE" unless $rc;

die $USAGE if exists $OPTIONS{help};

die "Must specify --infile\n$USAGE"
  unless exists $OPTIONS{infile};

open(IN,"$OPTIONS{infile}")
  or die "Couldn't open $OPTIONS{infile} for reading";

if (exists $OPTIONS{design}) {
  open(DESIGN,">$OPTIONS{design}")
    or die "Couldn't open $OPTIONS{design} for writing";
  print DESIGN "# id\ta_row\ta_col\trow\tcol\tname\n";
}

if (exists $OPTIONS{outfile}) {
  open(OUT,">$OPTIONS{outfile}")
    or die "Couldn't open $OPTIONS{outfile} for writing";
  print OUT "# id\ta_row\ta_col\trow\tcol\tname\n";
}


  # 0) Number
  # 1) Array Row
  # 2) Array Column
  # 3) Row
  # 4) Column
  # 5) Name
  # 6) X Location
  # 7) Y Location
  # 8) ch1 Intensity
  # 9) ch1 Background
  # 10) ch1 Intensity Std Dev
  # 11) ch1 Background Std Dev
  # 12) ch1 Diameter
  # 13) ch1 Area
  # 14) ch1 Footprint
  # 15) ch1 Circularity
  # 16) ch1 Spot Uniformity
  # 17) ch1 Bkg. Uniformity
  # 18) ch1 Signal Noise Ratio
  # 19) ch1 Confidence
  # 20) ch2 Intensity
  # 21) ch2 Background
  # 22) ch2 Intensity Std Dev
  # 23) ch2 Background Std Dev
  # 24) ch2 Diameter
  # 25) ch2 Area
  # 26) ch2 Footprint
  # 27) ch2 Circularity
  # 28) ch2 Spot Uniformity
  # 29) ch2 Bkg. Uniformity
  # 30) ch2 Signal Noise Ratio
  # 31) ch2 Confidence
  # 32) Ignore Filter

# all we need are:

  # 0) Number
  # 1) Array Row
  # 2) Array Column
  # 3) Row
  # 4) Column
  # 5) Name
  # 8) ch1 Intensity
  # 9) ch1 Background
  # 10) ch1 Intensity Std Dev
  # 11) ch1 Background Std Dev
  # 18) ch1 Signal Noise Ratio
  # 20) ch2 Intensity
  # 21) ch2 Background
  # 22) ch2 Intensity Std Dev
  # 23) ch2 Background Std Dev
  # 30) ch2 Signal Noise Ratio

my @INDICES = qw(0 1 2 3 4 5 8 9 10 11 18 20 21 22 23 30);

my ($ARRAY_ROWS,$ARRAY_COLS,$ROWS,$COLS,$TOTAL_SPOTS);
my $in_data;
my $data_start_regexp = qr/^Begin\s+Data/o;
my $reading_data;
my $reading_data_regexp = qr/^Number/;
my @spots;
my $count = 0;
while (<IN>) {
  # see if we've found the Data section already
  unless ($in_data or /$data_start_regexp/) {
    # if not grab the info from the header
    # Look for the following:
    #    Array Rows	12
    #    Array Columns	4
    #    Rows	10
    #    Columns	12
    #    Total Spots	5760		
    if (/^Array\s+Rows\s+(\d+)/) {
      $ARRAY_ROWS = $1;
    } elsif (/^Array\s+Columns\s+(\d+)/) {
      $ARRAY_COLS = $1;
    } elsif (/^Rows\s+(\d+)/) {
      $ROWS = $1;
    } elsif (/^Columns\s+(\d+)/) {
      $COLS = $1;
    } elsif (/^Total\s+Spots\s+(\d+)/) {
      $TOTAL_SPOTS = $1;
    }
    next;
  }

  # check if this is the beginning of the Data section
  if (/$data_start_regexp/) {
    $in_data = 1;
    die "Didn't find Array Rows\n"
      unless defined $ARRAY_ROWS;
    die "Didn't find Array Columns\n"
      unless defined $ARRAY_COLS;
    die "Didn't find Rows\n"
      unless defined $ROWS;
    die "Didn't find Columns\n"
      unless defined $COLS;
    die "Didn't find Total Spots\n"
      unless defined $TOTAL_SPOTS;
    next;
  }

  # don't proceed unless we've past the Data section header line
  next unless $reading_data or /$reading_data_regexp/;

  # check if this is the header line of the Data section
  if (/$reading_data_regexp/) {
    $reading_data = 1;
    next;
  }

  # when we reach the end of the Data section, we're done
  last if /^End/;

  # 0) Number
  # 1) Array Row
  # 2) Array Column
  # 3) Row
  # 4) Column
  # 5) Name
  # 8) ch1 Intensity
  # 9) ch1 Background
  # 10) ch1 Intensity Std Dev
  # 11) ch1 Background Std Dev
  # 18) ch1 Signal Noise Ratio
  # 20) ch2 Intensity
  # 21) ch2 Background
  # 22) ch2 Intensity Std Dev
  # 23) ch2 Background Std Dev
  # 30) ch2 Signal Noise Ratio

  my @data = split /\t/;
  my ($num,$a_row,$a_col,$row,$col,$name,
      $ch1_int, $ch1_bkg, $ch1_int_std, $ch1_bkg_std, $ch1_snr,
      $ch2_int, $ch2_bkg, $ch2_int_std, $ch2_bkg_std, $ch2_snr,
     ) = @data[@INDICES];

  # commence error checking
  die "Found strange array row: $a_row, for line: $num"
    unless defined $a_row and $a_row > 0 and $a_row <= $ARRAY_ROWS;
  die "Found strange array col: $a_col, for line: $num"
    unless defined $a_col and $a_col > 0 and $a_col <= $ARRAY_COLS;
  die "Found strange row: $row, for line: $num"
    unless defined $row and $row > 0 and $row <= $ROWS;
  die "Found strange col: $col, for line: $num"
    unless defined $col and $col > 0 and $col <= $COLS;

  push(@spots, [$num,$a_row,$a_col,$row,$col,$name,
      $ch1_int, $ch1_bkg, $ch1_int_std, $ch1_bkg_std, $ch1_snr,
      $ch2_int, $ch2_bkg, $ch2_int_std, $ch2_bkg_std, $ch2_snr,]
     );

  if ($OPTIONS{mangle}) {
    unless (lc($name) eq 'blank'
	    or lc($name) =~ /^negative/
	    or lc($name) =~ /^lambda/
	   ) {
      # fix the name
      $name = sprintf('reporter%05d', $count++);
    }
  } else {
    # only use the first name in a group (R78541 | R78475)
    $name =~ s/\s*|.*//;
  }

  if (exists $OPTIONS{design}) {
    my $id = "$a_row.$a_col.$row.$col";
    print DESIGN "$id\t$a_row\t$a_col\t$row\t$col\t$name\n";
  }
  if (exists $OPTIONS{outfile}) {
    $_ = join("\t",
	      $num,$a_row,$a_col,$row,$col,$name,
	      $ch1_int, $ch1_bkg, $ch1_int_std, $ch1_bkg_std, $ch1_snr,
	      $ch2_int, $ch2_bkg, $ch2_int_std, $ch2_bkg_std, $ch2_snr
	     );
  }
} continue {
  if (exists $OPTIONS{outfile}) {
    print OUT;
  }
}
die "Found strange number of spots: ",
  scalar @spots, " expected: $TOTAL_SPOTS\n"
  unless scalar @spots == $TOTAL_SPOTS;

print STDERR "Finished\n";

--- NEW FILE: tab2AD.pl ---
#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long;
use Bio::MAGE qw(:ALL);
use Bio::MAGE::XMLUtils;
use Benchmark;

my %OPTIONS;
my $rc = GetOptions(\%OPTIONS,
		    'infile=s',
		    'outfile=s',
		    'ad_identifier=s',
		    'fg_identifier=s',
		    'rg_identifier=s',
		    'help',
		   );

my $USAGE = <<"EOU";
usage: $0 [required flags] file1 ...
  required flags:
    --infile=file       : the tab-delimited file to read
    --outfile=file      : the array design XML file to create
    --ad_identifier=id  : the identifier to use for the ArrayDesign

  optional flags:
    --fg_identifier=id  : the identifier to use for the FeatureGroup
    --rg_identifier=id  : the identifier to use for the ReporterGroup
    --help              : print this message
EOU

die "Bad option\n$USAGE" unless $rc;

die $USAGE if exists $OPTIONS{help};

die "Must specify --infile\n$USAGE"
  unless exists $OPTIONS{infile};

die "Must specify --outfile\n$USAGE"
  unless exists $OPTIONS{outfile};

die "Must specify --identifier\n$USAGE"
  unless exists $OPTIONS{ad_identifier};

unless (exists $OPTIONS{fg_identifier}) {
  $OPTIONS{fg_identifier} =  $OPTIONS{ad_identifier};
  $OPTIONS{fg_identifier} =~ s/ArrayDesign/FeatureGroup/;
}

unless (exists $OPTIONS{rg_identifier}) {
  $OPTIONS{rg_identifier} =  $OPTIONS{ad_identifier};
  $OPTIONS{rg_identifier} =~ s/ArrayDesign/ReporterGroup/;
}

open(IN,"$OPTIONS{infile}")
  or die "Couldn't open $OPTIONS{infile} for reading";

open(OUT,">$OPTIONS{outfile}")
  or die "Couldn't open $OPTIONS{outfile} for writing";

my %zones;
my %reporters;
my $num_features;
my $cur_row = 0;
my $cur_col = 0;

my $start = new Benchmark;

my $zg = Bio::MAGE::ArrayDesign::ZoneGroup->new();
my $fg = Bio::MAGE::ArrayDesign::FeatureGroup->new(identifier=>"$OPTIONS{fg_identifier}",
							 );
my $rg = Bio::MAGE::ArrayDesign::ReporterGroup->new(identifier=>"$OPTIONS{rg_identifier}",
							 );

my $zone;
while (<IN>) {
  next if /^\#/;		# skip comment lines

  my ($id, $a_row, $a_col, $row, $col, $name) = split /\t/;
  my $zname = "$a_row.$a_col";

  # check that the zone exists
  my $zone = $zones{$zname};
  unless (defined $zone) {
    $zone = Bio::MAGE::ArrayDesign::Zone->new(identifier=>"Zone:$zname",
					      row=>$a_row,
					      column=>$a_col,
					     );
    $zones{$zname} = $zone;
    $zg->addZoneLocations($zone);
  }

  # create the Feature
  my $f_loc = Bio::MAGE::DesignElement::FeatureLocation->new(row=>$row,
							     column=>$col,
							    );
  my $feature = Bio::MAGE::DesignElement::Feature->new(identifier=>"$a_row.$a_col.$row.$col",
						       zone=>$zones{$zname},
						       featureLocation=>$f_loc,
						       );
  $fg->addFeatures($feature);

  # create a Reporter if necessary
  my $reporter = $reporters{$name};
  unless (defined $reporter) {
    $reporter = Bio::MAGE::DesignElement::Reporter->new(identifier=>"Reporter:$name",
							name=>$name,
						       );
    $rg->addReporters($reporter);
    $reporters{$name} = $reporter;
  }

  # create a FeatureReporterMap if necessary
  unless (defined $reporter->getFeatureReporterMaps()) {
    my $map = Bio::MAGE::DesignElement::FeatureReporterMap->new(identifier=>"FeatureReporterMap:$name");
    $map->setReporter($reporter);
    $reporter->addFeatureReporterMaps($map);
  }

  # map the Feature to the Reporter
  my $map_ref = $reporter->getFeatureReporterMaps();
  my $info = Bio::MAGE::DesignElement::FeatureInformation->new(feature=>$feature,
						       );
  $map_ref->[0]->addFeatureInformationSources($info);

  $num_features++;
  print "Completed $num_features\n" if $num_features % 1000 == 0;
}
print STDERR "Found $num_features features\n";
my $stop = new Benchmark;
my $diff = timediff($stop,$start);
print STDERR "Parsing took:", timestr($diff),"\n";
print STDERR "Found $num_features features\n";

my $ad = Bio::MAGE::ArrayDesign::PhysicalArrayDesign->new(identifier=>$OPTIONS{ad_identifier},
							  numberOfFeatures=>$num_features,
							  featureGroups=>[$fg],
							  reporterGroups=>[$rg],
							  zoneGroups=>[$zg],
							 );
print STDERR "Creating the MAGE object\n";
$start = new Benchmark;
my $mage = Bio::MAGE->new(identifier=>"MAGE-$OPTIONS{ad_identifier}",
			  objects=>[$ad]
			 );

$stop = new Benchmark;
$diff = timediff($stop,$start);
print STDERR "MAGE creation took:", timestr($diff),"\n";

print STDERR "Writing MAGE-ML\n";
$start = new Benchmark;

my $writer = Bio::MAGE::XMLWriter->new(fh=>\*OUT);
$writer->write($mage);

$stop = new Benchmark;
$diff = timediff($stop,$start);
print STDERR "Writing XML took:", timestr($diff),"\n";

print STDERR "Finished\n";

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genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 46)

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