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kuoi 2023-04-12 00:23:13 +08:00
parent cd056bb91b
commit 8092ada581
26 changed files with 11 additions and 6851 deletions
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6258
GDE2.0_manual.ps
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README.md Normal file
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# Genetic Data Environment
GDE is originally distributed under SunOS in the 1990s by [Eisen](https://doi.org/10.1385/0-89603-358-9:13).
This software is fixed from [Oliveira et al. (2003)](http://dx.doi.org/10.1093/bioinformatics/19.1.153) and re-distributed here.
# Usage
Though the dependency of GDE, xview, is orphaned by quite a lot of distributions, I still fix the software to give an outlook of how biologists worked during the last centenary.
To use it, you must install xview lib and include. xview hardly work well on x86_64 architecture.

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bin/Install.csh
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#/bin/csh
mkdir bin
#echo "Making blast..."
#cd BLAST
#Install.sh
#cd ..
echo "Making clustal..."
cd CLUSTAL
make
cd ..
echo "Making core GDE editor"
cd CORE
install.csh
cd ..
echo "Making FASTA"
cd FASTA
install.csh
cd ..
echo "Making Harvard Genome Lab functions"
cd HGL_SRC
install.csh
cd ..
echo "Making looptool"
cd LOOPTOOL
make
cd ..
echo "Making PHYLIP"
cd PHYLIP
install.csh
cd ..
echo "Making ReadSeq"
cd READSEQ
install.csh
cd ..
echo "Making other support programs"
cd SUPPORT
make
cd ..
echo "Making Zuker MFOLD"
cd ZUKER
install.csh
cd ..

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bin/Restriction
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bin/Zuk_to_gen
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bin/count
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bin/fasta2VESPA.pl
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#!/usr/bin/perl
##############################################################
# @author : Wagied Davids
# @progname : fasta2snap.pl
# @proglang : Perl script
# @purpose : Fasta to SNAP format converter
# @input : Fasta format files
# @output : SNAP format files
# @date : 05.08.2001
# @version : 0.001
##############################################################
use strict;
my ($fileIN,$fileOUT);
my ($de,@seq);
my $seq;
$fileIN= "infile";
#$fileOUT=" ";
open( FHIN, "$fileIN") || die "Error:$!";
#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
$/="%"; #input record seperator
while(<FHIN>){
($de,@seq)=split;
$seq=join("",@seq);
$seq= uc($seq);
$seq= substr($seq,0,-1); #> remaining at the end
print "$de\t\t$seq\n";
#print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
#print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
}
close(FHIN);
#close(FHOUT);

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bin/fasta2VESPA.pl~
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#!/usr/bin/perl
##############################################################
# @author : Wagied Davids
# @progname : fasta2snap.pl
# @proglang : Perl script
# @purpose : Fasta to SNAP format converter
# @input : Fasta format files
# @output : SNAP format files
# @date : 05.08.2001
# @version : 0.001
##############################################################
use strict;
my ($fileIN,$fileOUT);
my ($de,@seq);
my $seq;
$fileIN= "infile";
#$fileOUT=" ";
open( FHIN, "$fileIN") || die "Error:$!";
#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
$/="%"; #input record seperator
while(<FHIN>){
($de,@seq)=split;
$seq=join("",@seq);
$seq= uc($seq);
$seq= substr($seq,0,-1); #> remaining at the end
print "$de\t$seq\n";
#print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
#print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
}
close(FHIN);
#close(FHOUT);

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bin/fasta2snap.pl
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#!/usr/bin/perl
##############################################################
# @author : Wagied Davids
# @progname : fasta2snap.pl
# @proglang : Perl script
# @purpose : Fasta to SNAP format converter
# @input : Fasta format files
# @output : SNAP format files
# @date : 05.08.2001
# @version : 0.001
##############################################################
use strict;
my ($fileIN,$fileOUT);
my ($de,@seq);
my $seq;
$fileIN= "infile";
#$fileOUT=" ";
open( FHIN, "$fileIN") || die "Error:$!";
#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
$/="#"; #input record seperator
while(<FHIN>){
($de,@seq)=split;
$seq=join("",@seq);
$seq= uc($seq);
$seq= substr($seq,0,-1); #> remaining at the end
print "$de\t$seq\n";
#print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
#print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
}
close(FHIN);
#close(FHOUT);

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bin/fasta2snap.pl~
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#!/usr/bin/perl
##############################################################
# @author : Wagied Davids
# @progname : fasta2snap.pl
# @proglang : Perl script
# @purpose : Fasta to SNAP format converter
# @input : Fasta format files
# @output : SNAP format files
# @date : 05.08.2001
# @version : 0.001
##############################################################
use strict;
my ($fileIN,$fileOUT);
my ($de,@seq);
my $seq;
$fileIN= "infile";
#$fileOUT=" ";
open( FHIN, "$fileIN") || die "Error:$!";
#open( FHOUT, ">$fileOUT" ) || die "Error:$!";
$/=">"; #input record seperator
while(<FHIN>){
($de,@seq)=split;
$seq=join("",@seq);
$seq= uc($seq);
$seq= substr($seq,0,-1); #> remaining at the end
print "$de\t$seq\n";
#print FHOUT "<E><ID>$counter</ID<DE>$de</DE><SEQ>$seq</SEQ></E>\n";
#print FHOUT "<E><DE>$de</DE><SEQ>$seq</SEQ></E>\n";
}
close(FHIN);
#close(FHOUT);

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bin/installBLASTDB.pl
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#!/usr/bin/perl -w
use strict;
my $newFileName;
my $line;
my $sourceFile = shift;
my $menuName = shift;
print("mv -f ./$sourceFile.* /usr/local/bio/db/\n");
print("cp -f ./$sourceFile /usr/local/bio/db/\n");
print system("mv -f ./$sourceFile.* /usr/local/bio/db/");
# or die ("cannot copy files\n");
print system("cp -f ./$sourceFile /usr/local/bio/db/") ;
#or die ("cannot copy file\n");
open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^arg:BLASTDBDNA/){
print "FOUND\n";
while (<MENUFILE>){
print NEWFILE;
if (/^argchoice:/){
print NEWFILE "argchoice:$menuName:/usr/local/bio/db/$sourceFile\n";
last READLOOP;
}
}
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
print "new file: $newFileName\n";
system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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bin/installBLASTDB.pl~
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#!/usr/bin/perl -w
use strict;
my $newFileName;
my $line;
my $sourceFile = shift;
my $menuName = shift;
print("mv -f ./$sourceFile.* /usr/local/biotools/db/\n");
print("cp -f ./$sourceFile /usr/local/biotools/db/\n");
print system("mv -f ./$sourceFile.* /usr/local/biotools/db/");
# or die ("cannot copy files\n");
print system("cp -f ./$sourceFile /usr/local/biotools/db/") ;
#or die ("cannot copy file\n");
open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^arg:BLASTDBDNA/){
print "FOUND\n";
while (<MENUFILE>){
print NEWFILE;
if (/^argchoice:/){
print NEWFILE "argchoice:$menuName:/usr/local/biotools/db/$sourceFile\n";
last READLOOP;
}
}
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
print "new file: $newFileName\n";
system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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bin/installBLASTDBPROT.pl
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#!/usr/bin/perl -w
use strict;
my $newFileName;
my $line;
my $sourceFile = shift;
my $menuName = shift;
print("mv -f ./$sourceFile.* /usr/local/bio/db/\n");
print("cp -f ./$sourceFile /usr/local/bio/db/\n");
print system("mv -f ./$sourceFile.* /usr/local/bio/db/");
# or die ("cannot copy files\n");
print system("cp -f ./$sourceFile /usr/local/bio/db/") ;
#or die ("cannot copy file\n");
open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^arg:BLASTDBPROT/){
print "FOUND\n";
while (<MENUFILE>){
print NEWFILE;
if (/^argchoice:/){
print NEWFILE "argchoice:$menuName:/usr/local/bio/db/$sourceFile\n";
last READLOOP;
}
}
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
print "new file: $newFileName\n";
system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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bin/installBLASTDBPROT.pl~
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#!/usr/bin/perl -w
use strict;
my $newFileName;
my $line;
my $sourceFile = shift;
my $menuName = shift;
print("mv -f ./$sourceFile.* /usr/local/biotools/db/\n");
print("cp -f ./$sourceFile /usr/local/biotools/db/\n");
print system("mv -f ./$sourceFile.* /usr/local/biotools/db/");
# or die ("cannot copy files\n");
print system("cp -f ./$sourceFile /usr/local/biotools/db/") ;
#or die ("cannot copy file\n");
open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^arg:BLASTDBPROT/){
print "FOUND\n";
while (<MENUFILE>){
print NEWFILE;
if (/^argchoice:/){
print NEWFILE "argchoice:$menuName:/usr/local/biotools/db/$sourceFile\n";
last READLOOP;
}
}
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
print "new file: $newFileName\n";
system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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bin/newDATASET.pl
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#!/usr/bin/perl
my $name = shift;
my $file = shift;
open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^menu:seq. datasets/){
print "FOUND\n";
print NEWFILE "item:$name\n";
print NEWFILE "itemmethod:readseq /usr/local/bio/GDE/db/$file -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp\n";
print NEWFILE "out:OUTPUTFILE\n";
print NEWFILE "outformat:genbank\n\n";\
last READLOOP;
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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bin/newDATASET.pl~
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#!/usr/bin/perl
my $name = shift;
my $file = shift;
open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^menu:seq. datasets/){
print "FOUND\n";
print NEWFILE "item:$name\n";
print NEWFILE "itemmethod:readseq /usr/local/biotools/GDE/db/$file -a -f2 > OUTPUTFILE;/bin/rm -f OUTFILE.tmp\n";
print NEWFILE "out:OUTPUTFILE\n";
print NEWFILE "outformat:genbank\n\n";\
last READLOOP;
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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bin/newURL.pl
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#!/usr/bin/perl
my $urlname = shift;
my $url = shift;
open(MENUFILE, "/usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/bio/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^menu:On-Line/){
print "FOUND\n";
print NEWFILE "item:$urlname\n";
print NEWFILE "itemmethod:netscape $url &\n";
last READLOOP;
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
system("cp $newFileName /usr/local/bio/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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#!/usr/bin/perl
my $urlname = shift;
my $url = shift;
open(MENUFILE, "/usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot open menu file, sorry\n";
$newFileName = "/usr/local/biotools/GDE/CORE/.GDEmenusNew";
open(NEWFILE, ">$newFileName");
READLOOP:
while (<MENUFILE>){
print NEWFILE;
if (/^menu:On-Line/){
print "FOUND\n";
print NEWFILE "item:$urlname\n";
print NEWFILE "itemmethod:netscape $url &\n";
last READLOOP;
}
}
while (<MENUFILE>){
print NEWFILE;
}
close(NEWFILE);
close(MENUFILE);
system("cp $newFileName /usr/local/biotools/GDE/CORE/.GDEmenus")
or die "cannot replace old menu file\n";

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