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01AE2REI.pl
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01AE2REI.pl
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use File::Basename 'basename', 'dirname';
my $arrayfile = "/home/bono/AOE/99A.txt";
my $xrx2inst_file = "/home/bono/AOE/xRX2instrument_model.txt.gz";
#lookup arrayname for human being
open(FILE, $arrayfile) or die;
while(<FILE>) {
chomp;
my($id,$text) = split(/\t/);
$nameofarray{$id} = $text;
}
close FILE;
#lookup instrument_model for xRX
open(FILE, "zcat -dc $xrx2inst_file |") or die "$!: $xrx2inst_file\n";
while(<FILE>) {
chomp;
my ($xrx, $instrument_model) = split(/\t/);
$instrument_modelof{$xrx} = $instrument_model;
}
close FILE;
# print header line
print "ID\tDescription\tDate\tArrayType\tArrayGroup\tTechnology\tInstrument\tNGSGroup\tOrganisms\tRep_organism\n"; # organism
while(<STDIN>) { #idf file list from STDIN
chomp;
my $idf = $_;
my $id = '';
if($idf =~ /(E\-\w+\-\d+)/) {
$id = $1;
} else { next; }
my $exprdir = dirname $idf;
my $description = "";
my $prdate = "";
open(IDF, $idf) or die "$!:$idf\n";
my $line = '';
while(<IDF>) {
s/\r/\n/g;
$line .= $_;
}
close IDF;
foreach my $value (split(/\n/,$line)) {
my($zero) = split(/\t/,$value); #id
$value =~ s/^$zero\t//; #propery
$value =~ s/\t+//g; #remove a lot of \t
if($zero eq 'Investigation Title') {
$value =~ s/^\"//; $value =~ s/\"$//;
$description = $value;
}
$prdate = $value if($zero eq 'Public Release Date');
}
print "$id\t$description\t$prdate\t";
my $sdrf = "$exprdir/$id.sdrf.txt";
$sdrf = "$exprdir/$id.hyb.sdrf.txt" unless(-f $sdrf);
$sdrf = "$exprdir/$id.seq.sdrf.txt" unless(-f $sdrf);
unless(-f $sdrf) { print "\n"; next; }
my $i = 0;
my $i1 = undef;
my $i2 = undef;
my $i3 = undef;
my $i4 = undef;
my $maxorgno = 0;
my $rep_organism = '';
my $maxarrayno = 0;
my $rep_array = '';
my $instrumentmodel = '';
my $technologylist = '';
undef %marrays;
undef %organisms;
undef @values;
undef %technologies;
undef %instrumentmodels;
undef %ena_experiments;
open(SDRF, $sdrf) or die "$!:$sdrf\n";
while(<SDRF>) {
chomp;
my @values = split(/\t/);
if($i == 0) {
foreach my $value (@values) {
$i1 = $i if($value =~ /Array\s+Design\s+REF/i);
$i2 = $i if(($value =~ /Characteristics/i) && ($value =~ /\[Organism\]/i));
$i3 = $i if($value =~ /Technology\s+Type/i);
$i4 = $i if($value =~ /\[instrument_model\]/i);
$i5 = $i if($value =~ /\[ENA_EXPERIMENT\]/i);
$i++;
}
#last unless(defined($i1));
#last unless(defined($i2));
} else {
$values[$i1] =~ s/^\s+// if(defined($values[$i1])); #trim heading spaces
$values[$i2] =~ s/^\s+// if(defined($values[$i2])); #trim heading spaces
#$values[$i3] =~ s/^\s+//; #trim heading spaces
$values[$i1] =~ s/\"//g if(defined($values[$i1])); #trim double quotes
$values[$i2] =~ s/\"//g if(defined($values[$i2])); #trim double quotes
#$values[$i3] =~ s/\"//g; #trim double quotes
$marrays{$values[$i1]}++ if(($i1 > 0) && ($values[$i1] =~ /\w/)); #Array Design REF
$organisms{$values[$i2]}++ if(($i2 > 0) && ($values[$i2] =~ /\w/)); #Organism
$technologies{$values[$i3]}++ if(($i3 > 0) && ($values[$i3] =~ /\w/)); #Technology
$instrumentmodels{$values[$i4]}++ if(($i4 > 0) && ($values[$i4] =~ /\w/)); #instrument model
$ena_experiments{$values[$i5]}++ if(($i5 > 0) && ($values[$i5] =~ /\w/)); #ENA_EXPERIMENT
}
}
close SDRF;
foreach my $marray (keys %marrays) {
print "$nameofarray{$marray}($marray)\[$marrays{$marray}\] " if(defined($nameofarray{$marray}));
if( $marrays{$marray} > $maxarrayno){
$rep_array = $nameofarray{$marray};
$maxarrayno = $marrays{$marray};
}
}
print "\t";
if($rep_array =~ /affymetrix/i) { #arraygroup
print "Affymetrix\tarray assay\tNA\tNA";
} elsif($rep_array =~ /agilent/i) {
print "Agilent\tarray assay\tNA\tNA";
} else {# Other includes mostly NGS
print "Others\t";
foreach my $technology (keys %technologies) {
print "$technology ";
$technologylist .= $technology;
}
print "\t";
if($technologylist =~ /sequencing/i) { #NGS
my $instlist = '';
foreach $instrumentmodel (keys %instrumentmodels) {
$instlist .= $instrumentmodel;
}
# code for recent metadata
unless($instlist =~ /\w/) {
foreach my $xrx (keys %ena_experiments) {
#lookup instrument_model for xRX.
$instlist = $instrument_modelof{$xrx}; # not deal with multiple sequencer in the same xRX
}
}
print "$instlist";
if($instlist =~ /illumina/i) {
$ngsgroup = "Illumina";
} else {
$ngsgroup = "Others";
}
print "\t$ngsgroup";
} else { # no NGS
print "\tNA";
}
}
print "\t";
foreach my $organism (keys %organisms) {
print "$organism\[$organisms{$organism}\] ";
if( $organisms{$organism} > $maxorgno){
$rep_organism = $organism;
$maxorgno = $organisms{$organism};
}
}
print "\t";
print "$rep_organism";
print "\n";
}
exit 0;