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|
#!/usr/bin/perl
#############################################################
# filterGenes
# filter genes from a genbank flat file database
# usage: fileterGenes namefile dbfile
#
#
# Mario Stanke, 13.08.2002
#############################################################
if ($#ARGV != 1) {
print "usage:filterGenes namefile dbfile\n";
print "names of the mRNAs to be discarded from\n";
print "the first parameter.\n";
exit;
}
$origfilename = $ARGV[1];
$goodfilename = $ARGV[0];
open(origfile, "$origfilename") || die "Couldn't open dbfile\n";
@data = <origfile>;
close(origfile);
$/="\n//\n";
my $head;
my $mRNAflag = 0;
my $cdsFlag = 0;
my $genename;
my $printFlag = 0;
my $firstPrintFlag = 0;
foreach(@data) {
if($_=~m/^LOCUS/){
$head = "";
$printFlag = 0;
$genename = "";
$head = $head.$_;
}
if($_=~m/FEATURES/){
$head = $head.$_;
}
if($_=~m/source/){
$head = $head.$_;
}
if($mRNAflag==1 and not($_=~m/CDS/)){
$head = $head.$_;
}
if($_=~m/mRNA/){
$mRNAflag = 1;
$head = $head.$_;
}
if($cdsFlag==1){
if($_=~m/gene="/){
@tmp = split(/\"/);
$genename = $tmp[1];
$cdsFlag = 0;
$firstPrintFlag = 1;
}else{
$head = $head.$_;
}
}
if($_=~m/CDS/){
$mRNAflag = 0;
$head = $head.$_;
$cdsFlag = 1;
}
if($firstPrintFlag==1 and length($head)>=2){
#checks whether a gene name exists in reference file
@line = `grep $genename $goodfilename`;
if(length($line[0])<1){
#print "Got into head printing $genename\n";
print $head;
$head = "";
$printFlag = 1;
}
$firstPrintFlag = 0;
@line = ();
}
if($printFlag==1){
#print "Got into body printing $genename\n";
print $_;
}
}
|
