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Commit 691e045e authored by Sebastien Moretti's avatar Sebastien Moretti
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Fix paths

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cgi-bin/EPD2NICE.pl
+ 9
− 9
View file @ 691e045e
......@@ -423,16 +423,16 @@ while (<RECORD>)
# determine if link to NCBI Genome Map possible
if ($taxID{$OS1}){
# determine latest BED file for this organism
open(BED, "ls -t /db/ftp/epd/BED | grep $assemb{$OS1} |") or warn ("error determining BED: $!\n");
#print "ls -t /db/ftp/epd/BED | grep $assemb{$OS1} |";
open(BED, "ls -t /home/local/ftp/epd/BED | grep $assemb{$OS1} |") or warn ("error determining BED: $!\n");
#print "ls -t /home/local/ftp/epd/BED | grep $assemb{$OS1} |";
my $BED=<BED>;
close(BED);
my $nBED=(split(/\n/,$BED))[0];
#print "my bed = $nBED";
if ($nBED ne ''){
# grep BED file to determine position
open(POS, "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$nBED |") or warn ("error opening grep: $!\n");
#print "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$nBED |";
open(POS, "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$nBED |") or warn ("error opening grep: $!\n");
#print "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$nBED |";
my $test=<POS>;
close(POS);
if ((split(/\n/,$test))[0]){
......@@ -458,8 +458,8 @@ ALT: print "\t\t\t\t\t<td bgcolor\=\"\#FFFFCC\"><a href=\"$URLs{GENOME}$GE_S
}
# determine if links to Genome Browsers possible
if ($ENSEMBL{$OS1}){
open(POS, "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$BEDE{$OS1} |") or warn ("error opening grep: $!\n");
#print "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$BEDE{$OS1}";
open(POS, "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$BEDE{$OS1} |") or warn ("error opening grep: $!\n");
#print "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$BEDE{$OS1}";
my $test=<POS>;
close(POS);
if ((split(/\n/,$test))[0]){
......@@ -473,7 +473,7 @@ ALT: print "\t\t\t\t\t<td bgcolor\=\"\#FFFFCC\"><a href=\"$URLs{GENOME}$GE_S
}
}
if ($UCSC{$OS1}){
open(POS, "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$BEDU{$OS1} |") or warn ("error opening grep: $!\n");
open(POS, "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$BEDU{$OS1} |") or warn ("error opening grep: $!\n");
my $test=<POS>;
close(POS);
if ((split(/\n/,$test))[0]){
......@@ -487,7 +487,7 @@ ALT: print "\t\t\t\t\t<td bgcolor\=\"\#FFFFCC\"><a href=\"$URLs{GENOME}$GE_S
}
}
if ($PlantGDB{$OS1}){
open(POS, "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$BEDP{$OS1} |") or warn ("error opening grep: $!\n");
open(POS, "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$BEDP{$OS1} |") or warn ("error opening grep: $!\n");
my $test=<POS>;
close(POS);
if ((split(/\n/,$test))[0]){
......@@ -505,7 +505,7 @@ ALT: print "\t\t\t\t\t<td bgcolor\=\"\#FFFFCC\"><a href=\"$URLs{GENOME}$GE_S
if ($OS1 eq 'Homo sapiens') {
## grep old BED file to determine position +/-200bp # remove once HapMap updated to NCBI36
# open(POS, "grep \$\'\t$ID\t\' /db/ftp/epd/BED/$BEDP{$OS1} |") or warn ("error opening epd85_HS_NCBI35.BED: $!\n");
# open(POS, "grep \$\'\t$ID\t\' /home/local/ftp/epd/BED/$BEDP{$OS1} |") or warn ("error opening epd85_HS_NCBI35.BED: $!\n");
# my $test=<POS>;
# close(POS);
# my ($chro, $gpos);
......
cgi-bin/epdTxt2HTML.pl
+ 6
− 6
View file @ 691e045e
......@@ -84,13 +84,13 @@ elsif (/^DR GENOME/)
# determine if link to NCBI Genome Map possible
if ($taxID{$OS1}){
# determine latest BED file for this organism (to retrieve chromosome number!)
open(BED, "ls -t /db/ftp/epd/BED|grep $assemb{$OS1} |") or warn ("error determining BED: $!\n");
open(BED, "ls -t /home/local/ftp/epd/BED|grep $assemb{$OS1} |") or warn ("error determining BED: $!\n");
my $BED=<BED>;
close(BED);
my $nBED=(split(/\n/,$BED))[0];
if ($nBED ne ''){
# grep BED file to determine position
open(POS, "grep \'\t$gID\t\' /db/ftp/epd/BED/$nBED |") or warn ("error opening grep: $!\n");
open(POS, "grep \'\t$gID\t\' /home/local/ftp/epd/BED/$nBED |") or warn ("error opening grep: $!\n");
my $test=<POS>;
close(POS);
if ((split(/\n/,$test))[0]){
......@@ -116,7 +116,7 @@ ALT: print "DR GENOME\; <a href\=\"$URLs{GENOME}$sv\">$sv<\/a>$suite [";
}
# determine if links to Genome Browsers possible
if ($ENSEMBL{$OS1}){
open(POS, "grep \'\t$gID\t\' /db/ftp/epd/BED/$BEDE{$OS1} |") or warn ("error opening grep: $!\n");
open(POS, "grep \'\t$gID\t\' /home/local/ftp/epd/BED/$BEDE{$OS1} |") or warn ("error opening grep: $!\n");
my @test=<POS>;
close(POS);
if ($test[0]){
......@@ -130,7 +130,7 @@ ALT: print "DR GENOME\; <a href\=\"$URLs{GENOME}$sv\">$sv<\/a>$suite [";
}
}
if ($UCSC{$OS1}){
open(POS, "grep \'\t$gID\t\' /db/ftp/epd/BED/$BEDU{$OS1} |") or warn ("error opening grep: $!\n");
open(POS, "grep \'\t$gID\t\' /home/local/ftp/epd/BED/$BEDU{$OS1} |") or warn ("error opening grep: $!\n");
my @test=<POS>;
close(POS);
if ($test[0]){
......@@ -146,7 +146,7 @@ ALT: print "DR GENOME\; <a href\=\"$URLs{GENOME}$sv\">$sv<\/a>$suite [";
}
}
if ($PlantGDB{$OS1}){
open(POS, "grep \'\t$gID\t\' /db/ftp/epd/BED/$BEDP{$OS1} |") or warn ("error opening grep: $!\n");
open(POS, "grep \'\t$gID\t\' /home/local/ftp/epd/BED/$BEDP{$OS1} |") or warn ("error opening grep: $!\n");
my $test=<POS>;
close(POS);
if ((split(/\n/,$test))[0]){
......@@ -159,7 +159,7 @@ ALT: print "DR GENOME\; <a href\=\"$URLs{GENOME}$sv\">$sv<\/a>$suite [";
}
if ($OS1 eq 'Homo sapiens') {
## grep old BED file to determine position +/-200bp # remove once HapMap updated to NCBI36
# open(POS, "grep \'\t$gID\t\' /db/ftp/epd/BED/epd85_HS_NCBI35.BED |") or warn ("error opening epd85_HS_NCBI35.BED: $!\n");
# open(POS, "grep \'\t$gID\t\' /home/local/ftp/epd/BED/epd85_HS_NCBI35.BED |") or warn ("error opening epd85_HS_NCBI35.BED: $!\n");
# my @test=<POS>;
# close(POS);
# if ($test[0]){
......
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