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|
#!/usr/bin/perl -w
%databases = (
"embl" => "embl embl embl acc [.]dat\$",
"genbank" => "genbank genbank gb acc [.]seq\$",
"swiss" => "swiss sw sw acc [.]dat\$",
"pir" => "pir pir pir id [.]ref\$",
"swnew" => "swnew swnew sw acc [.]dat\$"
);
foreach $d (sort( keys(%databases))) {
my ($dir, $db,$fmt,$field, $fname) = split (/ /, $databases{$d});
my $srsdb;
print "$d: '$dir' '$db' '$fmt' '$field' '$fname'\n";
opendir(DIR, $dir);
while($file = readdir(DIR)) {
if($file !~ $fname) {next}
print ("\n $file\n");
open(IN, "$dir/$file") || die "Cannot open $dir/$file";
$ac=0;
$allok = 1;
$change=0;
if(-e "newfile") {system "rm newfile;touch newfile";}
if($fmt eq "pir") {
if(-e "newfile2") {system "rm newfile2;touch newfile2";}
}
if($file eq "est.dat") {$srsdb = $db."est"}
elsif($file eq "condiv.dat") {$srsdb = $db."con"}
elsif($file eq "wgs.dat") {$srsdb = $db."wgs"}
else {$srsdb = $db}
while (<IN>) {
$id="";
if($fmt eq "embl") {
if(/^AC +([^ ;\n]+)/) {
if(!$ac++){$id = $1}}
else {$ac=0}
}
elsif($fmt eq "sw") {
if(/^AC +([^ ;\n]+)/) {if(!$ac++){$id = $1}}
else {$ac=0}
}
elsif($fmt eq "gb") {
if(/^ACCESSION +([^ ;\n]+)/) {$id = $1}
}
elsif($fmt eq "pir") {
if(/^>..;([^ ;\n]+)/) {$id = $1}
}
if($id eq "") {next}
print " id:$id";
$istatus = system "EMBOSSRC=./dbfetch/ ;export EMBOSSRC ;EMBOSS_RCHOME=N ;export EMBOSS_RCHOME ;entret -auto t$db\-$field:$id x.x";
$jstatus = system "EMBOSSRC=./dbfetch ;export EMBOSSRC ;EMBOSS_RCHOME=N ;export EMBOSS_RCHOME ;entret -auto srs$srsdb\-$field:$id y.y";
if(!$jstatus && $fmt eq "pir") {
$file2 = $file;
$file2 =~ s/[.]ref/.seq/g;
open (Y, "y.y");
open (W, ">w.w");
my $pirseq = "";
my $pircount = 0;
my $pirlines = 0;
my $isseq = 0;
while(<Y>) {
print W;
if(/^>/) {$pircount++;$pirlines=0}
else {$pirlines++}
if($pircount == 2){
if($pirlines < 2) {next}
$isseq = 1;
s/\s//g;
}
$pirseq .= $_;
}
if($isseq) {$pirseq .= "\n"}
close Y;
close W;
open (Y, ">y.y");
print Y $pirseq;
close Y;
}
system "diff x.x y.y > z.z";
if($istatus) {
print " current failed $istatus\n";
$allok = 0;
}
elsif($jstatus) {
print " latest failed $jstatus\n";
$allok = 0;
}
elsif(-s "z.z") {
printf " diff %d %d %d\n", (-s "z.z"), (-s "x.x"), (-s "y.y");
$change=1;
if($fmt eq "pir") {
open (Z, "z.z");
while(<Z>) {print}
close Z;
open (REF, ">>newfile");
open (SEQ, ">>newfile2");
open (Y, "y.y");
$ref = 0;
$seq=0;
@pirseq = ();
while(<Y>) {
if(/^>/) {
$ref++;
if($ref == 1) {$saveref = $_}
if($ref == 2) {$_ = $saveref}
}
if($ref < 2) {
print REF;
}
else {
$seq++;
if($seq <= 2) {
print SEQ;
}
else {
chomp;
push @pirseq, split (/\s+/, $_);
}
}
}
foreach $p (@pirseq) {
# if($j++ == 8) {
# $j=0;
# print SEQ "\n";
# }
print SEQ "$p";
}
print SEQ "\n";
close REF;
close SEQ;
close Y;
}
else {
system "cat y.y >> newfile";
}
}
else {
print " OK\n";
if($fmt eq "pir") {
open (REF, ">>newfile");
open (SEQ, ">>newfile2");
open (Y, "w.w");
$ref = 0;
$seq=0;
@pirseq = ();
while(<Y>) {
if(/^>/) {
$ref++;
if($ref == 1) {$saveref = $_}
if($ref == 2) {$_ = $saveref}
}
if($ref < 2) {
print REF;
}
else {
$seq++;
if($seq <= 2) {
print SEQ;
}
else {
push @pirseq, split (/\s+/, $_);
}
}
}
foreach $p (@pirseq) {
print SEQ "$p";
}
print SEQ "\n";
close REF;
close SEQ;
close Y;
}
else {
system "cat y.y >> newfile";
}
}
}
close(IN);
if($allok && $change) {
$replace++;
printf "REPLACE $dir/$file %d %d\n", (-s "$dir/$file"), (-s "newfile");
system "cp newfile $dir/$file";
if($fmt eq "pir") {
printf "REPLACE $dir/$file2 %d %d\n", (-s "$dir/$file2"), (-s "newfile2");
system "cp newfile2 $dir/$file2";
}
}
elsif($allok) {
system "diff $dir/$file newfile > z.z";
if(-s "z.z") {
printf "KEEP but size changed %d %d %d\n",
(-s "$db/$file"), (-s "newfile"), (-s "z.z");
}
else {
print "KEEP unchanged\n";
}
if($fmt eq "pir") {
system "diff $dir/$file2 newfile2 > z.z";
if(-s "z.z") {
$replace++;
printf "KEEP but REF size changed %d %d %d\n",
(-s "$db/$file"), (-s "newfile"), (-s "z.z");
}
}
}
else {
print "PROBLEM somewhere\n";
}
}
}
if($replace) {
print "Replaced $replace databases\n";
}
else {
print "ALL UNCHANGED\n";
}
|
