目录
序言
基因组学是一门研究基因组的科学，它涉及到基因组的结构，功能，表达，进化和疾病相关性等方面。基因组学的研究需要大量的基因数据，而这些数据可以从公共数据库中获得。
其中最常用的数据库是GEO（Gene Expression Omnibus），它提供了大量的基因表达数据，可以用于基因组学研究。 GEO数据库中的数据可以通过FTP或Web界面下载，下载的数据可以是原始数据，也可以是已经注释的数据。
下载的原始数据需要进行注释，以便更好地理解和分析数据。GEO数据库中的数据可以使用多种注释工具进行注释，如NCBI的GeneInfo，Ensembl，UniProt，KEGG，GO等。
本文将介绍如何从GEO数据库中下载基因数据，以及如何使用不同的注释工具对数据进行注释。首先，我们将介绍如何从GEO数据库中下载基因数据，包括如何搜索和下载数据，以及如何解压缩下载的数据。然后，我们将介绍如何使用不同的注释工具对数据进行注释，包括NCBI的GeneInfo，Ensembl，UniProt，KEGG，GO等。
最后，我们将介绍如何使用ANN技术对基因数据进行分析，以及如何利用注释的基因数据进行生物信息学研究。
GEO数据下载
https://www.ncbi.nlm.nih.gov/geo/
搜索关键字：gastric cancer
下载两个文件，平台文件和基因表达矩阵
基因表达文件名为GSE54129_series_matrix.txt
探针文件名字改成GPL570-55999.txt
GEO数据注释
对GEO数据库中的数据进行详细的解释和描述，以便更好地理解基因表达的调控机制。GEO数据注释可以帮助研究人员更好地分析和理解GEO数据库中的数据，从而更好地利用GEO数据库中的数据进行研究。
流程如下：
将基因表达文件改名为ann.txt 探针文件名字改成probe.txt
将perl脚本放下去
先查看ann.txt中基因名称是第几列，在第11列
打开cmd终端 输入perl 脚本名字即可注释完成
输入基因的名字在哪一列
得到geneMatrix.txt改名为GSE54129.txt，即是注释好的文件
脚本代码如下：
#!/usr/bin/perl
#line 2 "C:\Strawberry\perl\site\bin\par.pl"
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
package __par_pl;
# --- This script must not use any modules at compile time ---
# use strict;
#line 156
my ($PAR_MAGIC, $par_temp, $progname, @tmpfile, %ModuleCache);
END { if ($ENV{PAR_CLEAN}) {
require File::Temp;
require File::Basename;
require File::Spec;
my $topdir = File::Basename::dirname($par_temp);
outs(qq[Removing files in "$par_temp"]);
File::Find::finddepth(sub { ( -d ) ? rmdir : unlink }, $par_temp);
rmdir $par_temp;
# Don't remove topdir because this causes a race with other apps
# that are trying to start.
if (-d $par_temp && $^O ne 'MSWin32') {
# Something went wrong unlinking the temporary directory. This
# typically happens on platforms that disallow unlinking shared
# libraries and executables that are in use. Unlink with a background
# shell command so the files are no longer in use by this process.
# Don't do anything on Windows because our parent process will
# take care of cleaning things up.
my $tmp = new File::Temp(
TEMPLATE => 'tmpXXXXX',
DIR => File::Basename::dirname($topdir),
SUFFIX => '.cmd',
UNLINK => 0,
);
my $filename = $tmp->filename;
print $tmp <<"...";
#!/bin/sh
x=1; while [ \$x -lt 10 ]; do
rm -rf '$par_temp'
if [ \! -d '$par_temp' ]; then
break
fi
sleep 1
x=`expr \$x + 1`
done
rm '$filename'
...
close $tmp;
chmod 0700, $filename;
my $cmd = "$filename >/dev/null 2>&1 &";
system($cmd);
outs(qq[Spawned background process to perform cleanup: $filename]);
}
} }
BEGIN {
Internals::PAR::BOOT() if defined &Internals::PAR::BOOT;
$PAR_MAGIC = "\nPAR.pm\n";
eval {
_par_init_env();
my $quiet = !$ENV{PAR_DEBUG};
# fix $progname if invoked from PATH
my %Config = (
path_sep => ($^O =~ /^MSWin/ ? ';' : ':'),
_exe => ($^O =~ /^(?:MSWin|OS2|cygwin)/ ? '.exe' : ''),
_delim => ($^O =~ /^MSWin|OS2/ ? '\\' : '/'),
);
_set_progname();
_set_par_temp();
# Magic string checking and extracting bundled modules {{{
my ($start_pos, $data_pos);
{
local $SIG{__WARN__} = sub {};
# Check file type, get start of data section {{{
open _FH, '<:raw', $progname or last;
# Search for the "\nPAR.pm\n signature backward from the end of the file
my $buf;
my $size = -s $progname;
my $chunk_size = 64 * 1024;
my $magic_pos;
if ($size <= $chunk_size) {
$magic_pos = 0;
} elsif ((my $m = $size % $chunk_size) > 0) {
$magic_pos = $size - $m;
} else {
$magic_pos = $size - $chunk_size;
}
# in any case, $magic_pos is a multiple of $chunk_size
while ($magic_pos >= 0) {
seek _FH, $magic_pos, 0;
read _FH, $buf, $chunk_size + length($PAR_MAGIC);
if ((my $i = rindex($buf, $PAR_MAGIC)) >= 0) {
$magic_pos += $i;
last;
}
$magic_pos -= $chunk_size;
}
last if $magic_pos < 0;
# Seek 4 bytes backward from the signature to get the offset of the
# first embedded FILE, then seek to it
seek _FH, $magic_pos - 4, 0;
read _FH, $buf, 4;
seek _FH, $magic_pos - 4 - unpack("N", $buf), 0;
$data_pos = tell _FH;
# }}}
# Extracting each file into memory {{{
my %require_list;
read _FH, $buf, 4; # read the first "FILE"
while ($buf eq "FILE") {
read _FH, $buf, 4;
read _FH, $buf, unpack("N", $buf);
my $fullname = $buf;
outs(qq[Unpacking FILE "$fullname"...]);
my $crc = ( $fullname =~ s|^([a-f\d]{8})/|| ) ? $1 : undef;
my ($basename, $ext) = ($buf =~ m|(?:.*/)?(.*)(\..*)|);
read _FH, $buf, 4;
read _FH, $buf, unpack("N", $buf);
if (defined($ext) and $ext !~ /\.(?:pm|pl|ix|al)$/i) {
my $filename = _save_as("$crc$ext", $buf, 0755);
$PAR::Heavy::FullCache{$fullname} = $filename;
$PAR::Heavy::FullCache{$filename} = $fullname;
}
elsif ( $fullname =~ m|^/?shlib/| and defined $ENV{PAR_TEMP} ) {
my $filename = _save_as("$basename$ext", $buf, 0755);
outs("SHLIB: $filename\n");
}
else {
$require_list{$fullname} =
$ModuleCache{$fullname} = {
buf => $buf,
crc => $crc,
name => $fullname,
};
}
read _FH, $buf, 4;
}
# }}}
local @INC = (sub {
my ($self, $module) = @_;
return if ref $module or !$module;
my $info = delete $require_list{$module} or return;
$INC{$module} = "/loader/$info/$module";
if ($ENV{PAR_CLEAN} and defined(&IO::File::new)) {
my $fh = IO::File->new_tmpfile or die "Can't create temp file: $!";
$fh->binmode();
$fh->print($info->{buf});
$fh->seek(0, 0);
return $fh;
}
else {
my $filename = _save_as("$info->{crc}.pm", $info->{buf});
open my $fh, '<:raw', $filename or die qq[Can't read "$filename": $!];
return $fh;
}
die "Bootstrapping failed: can't find module $module!";
}, @INC);
# Now load all bundled files {{{
# initialize shared object processing
require XSLoader;
require PAR::Heavy;
require Carp::Heavy;
require Exporter::Heavy;
PAR::Heavy::_init_dynaloader();
# now let's try getting helper modules from within
require IO::File;
# load rest of the group in
while (my $filename = (sort keys %require_list)[0]) {
#local $INC{'Cwd.pm'} = __FILE__ if $^O ne 'MSWin32';
unless ($INC{$filename} or $filename =~ /BSDPAN/) {
# require modules, do other executable files
if ($filename =~ /\.pmc?$/i) {
require $filename;
}
else {
# Skip ActiveState's sitecustomize.pl file:
do $filename unless $filename =~ /sitecustomize\.pl$/;
}
}
delete $require_list{$filename};
}
# }}}
last unless $buf eq "PK\003\004";
$start_pos = (tell _FH) - 4; # start of zip
}
# }}}
# Argument processing {{{
my @par_args;
my ($out, $bundle, $logfh, $cache_name);
delete $ENV{PAR_APP_REUSE}; # sanitize (REUSE may be a security problem)
$quiet = 0 unless $ENV{PAR_DEBUG};
# Don't swallow arguments for compiled executables without --par-options
if (!$start_pos or ($ARGV[0] eq '--par-options' && shift)) {
my %dist_cmd = qw(
p blib_to_par
i install_par
u uninstall_par
s sign_par
v verify_par
);
# if the app is invoked as "appname --par-options --reuse PROGRAM @PROG_ARGV",
# use the app to run the given perl code instead of anything from the
# app itself (but still set up the normal app environment and @INC)
if (@ARGV and $ARGV[0] eq '--reuse') {
shift @ARGV;
$ENV{PAR_APP_REUSE} = shift @ARGV;
}
else { # normal parl behaviour
my @add_to_inc;
while (@ARGV) {
$ARGV[0] =~ /^-([AIMOBLbqpiusTv])(.*)/ or last;
if ($1 eq 'I') {
push @add_to_inc, $2;
}
elsif ($1 eq 'M') {
eval "use $2";
}
elsif ($1 eq 'A') {
unshift @par_args, $2;
}
elsif ($1 eq 'O') {
$out = $2;
}
elsif ($1 eq 'b') {
$bundle = 'site';
}
elsif ($1 eq 'B') {
$bundle = 'all';
}
elsif ($1 eq 'q') {
$quiet = 1;
}
elsif ($1 eq 'L') {
open $logfh, ">>", $2 or die qq[Can't open log file "$2": $!];
}
elsif ($1 eq 'T') {
$cache_name = $2;
}
shift(@ARGV);
if (my $cmd = $dist_cmd{$1}) {
delete $ENV{'PAR_TEMP'};
init_inc();
require PAR::Dist;
&{"PAR::Dist::$cmd"}() unless @ARGV;
&{"PAR::Dist::$cmd"}($_) for @ARGV;
exit;
}
}
unshift @INC, @add_to_inc;
}
}
# XXX -- add --par-debug support!
# }}}
# Output mode (-O) handling {{{
if ($out) {
{
#local $INC{'Cwd.pm'} = __FILE__ if $^O ne 'MSWin32';
require IO::File;
require Archive::Zip;
require Digest::SHA;
}
my $par = shift(@ARGV);
my $zip;
if (defined $par) {
open my $fh, '<:raw', $par or die qq[Can't find par file "$par": $!];
bless($fh, 'IO::File');
$zip = Archive::Zip->new;
( $zip->readFromFileHandle($fh, $par) == Archive::Zip::AZ_OK() )
or die qq[Error reading zip archive "$par"];
}
my %env = do {
if ($zip and my $meta = $zip->contents('META.yml')) {
$meta =~ s/.*^par:$//ms;
$meta =~ s/^\S.*//ms;
$meta =~ /^ ([^:]+): (.+)$/mg;
}
};
# Open input and output files {{{
if (defined $par) {
open my $ph, '<:raw', $par or die qq[Can't read par file "$par": $!];
my $buf;
read $ph, $buf, 4;
die qq["$par" is not a par file] unless $buf eq "PK\003\004";
close $ph;
}
CreatePath($out) ;
my $fh = IO::File->new(
$out,
IO::File::O_CREAT() | IO::File::O_WRONLY() | IO::File::O_TRUNC(),
0777,
) or die qq[Can't create file "$out": $!];
$fh->binmode();
seek _FH, 0, 0;
my $loader;
if (defined $data_pos) {
read _FH, $loader, $data_pos;
} else {
local $/ = undef;
$loader = <_FH>;
}
if (!$ENV{PAR_VERBATIM} and $loader =~ /^(?:#!|\@rem)/) {
require PAR::Filter::PodStrip;
PAR::Filter::PodStrip->apply(\$loader, $0);
}
foreach my $key (sort keys %env) {
my $val = $env{$key} or next;
$val = eval $val if $val =~ /^['"]/;
my $magic = "__ENV_PAR_" . uc($key) . "__";
my $set = "PAR_" . uc($key) . "=$val";
$loader =~ s{$magic( +)}{
$magic . $set . (' ' x (length($1) - length($set)))
}eg;
}
$fh->print($loader);
# }}}
# Write bundled modules {{{
if ($bundle) {
require PAR::Heavy;
PAR::Heavy::_init_dynaloader();
init_inc();
require_modules();
my @inc = grep { !/BSDPAN/ }
grep {
($bundle ne 'site') or
($_ ne $Config::Config{archlibexp} and
$_ ne $Config::Config{privlibexp});
} @INC;
# normalize paths (remove trailing or multiple consecutive slashes)
s|/+|/|g, s|/$|| foreach @inc;
# Now determine the files loaded above by require_modules():
# Perl source files are found in values %INC and DLLs are
# found in @DynaLoader::dl_shared_objects.
my %files;
$files{$_}++ for @DynaLoader::dl_shared_objects, values %INC;
my $lib_ext = $Config::Config{lib_ext}; # XXX lib_ext vs dlext ?
my %written;
foreach my $key (sort keys %files) {
my ($file, $name);
if (defined(my $fc = $PAR::Heavy::FullCache{$key})) {
($file, $name) = ($key, $fc);
}
else {
foreach my $dir (@inc) {
if ($key =~ m|^\Q$dir\E/(.*)$|i) {
($file, $name) = ($key, $1);
last;
}
if ($key =~ m|^/loader/[^/]+/(.*)$|) {
if (my $ref = $ModuleCache{$1}) {
($file, $name) = ($ref, $1);
last;
}
if (-f "$dir/$1") {
($file, $name) = ("$dir/$1", $1);
last;
}
}
}
}
# There are legitimate reasons why we couldn't find $name and $file for a $key:
# - cperl has e.g. $INC{"XSLoader.pm"} = "XSLoader.c",
# $INC{"DynaLoader.pm"}' = "dlboot_c.PL"
next unless defined $name;
next if $written{$name}++;
next if !ref($file) and $file =~ /\.\Q$lib_ext\E$/i;
outs(sprintf(qq[Packing FILE "%s"...], ref $file ? $file->{name} : $file));
my $content;
if (ref($file)) {
$content = $file->{buf};
}
else {
local $/ = undef;
open my $fh, '<:raw', $file or die qq[Can't read "$file": $!];
$content = <$fh>;
close $fh;
PAR::Filter::PodStrip->apply(\$content, "<embedded>/$name")
if !$ENV{PAR_VERBATIM} and $name =~ /\.(?:pm|ix|al)$/i;
PAR::Filter::PatchContent->new->apply(\$content, $file, $name);
}
$fh->print("FILE",
pack('N', length($name) + 9),
sprintf("%08x/%s", Archive::Zip::computeCRC32($content), $name),
pack('N', length($content)),
$content);
outs(qq[Written as "$name"]);
}
}
# }}}
# Now write out the PAR and magic strings {{{
$zip->writeToFileHandle($fh) if $zip;
$cache_name = substr $cache_name, 0, 40;
if (!$cache_name and my $mtime = (stat($out))[9]) {
my $ctx = Digest::SHA->new(1);
open my $fh, "<:raw", $out;
$ctx->addfile($fh);
close $fh;
$cache_name = $ctx->hexdigest;
}
$cache_name .= "\0" x (41 - length $cache_name);
$cache_name .= "CACHE";
$fh->print($cache_name);
$fh->print(pack('N', $fh->tell - length($loader)));
$fh->print($PAR_MAGIC);
$fh->close;
chmod 0755, $out;
# }}}
exit;
}
# }}}
# Prepare $progname into PAR file cache {{{
{
last unless defined $start_pos;
_fix_progname();
# Now load the PAR file and put it into PAR::LibCache {{{
require PAR;
PAR::Heavy::_init_dynaloader();
{
#local $INC{'Cwd.pm'} = __FILE__ if $^O ne 'MSWin32';
require File::Find;
require Archive::Zip;
}
my $fh = IO::File->new; # Archive::Zip operates on an IO::Handle
$fh->fdopen(fileno(_FH), 'r') or die qq[fdopen() failed: $!];
# Temporarily increase the chunk size for Archive::Zip so that it will find the EOCD
# even if lots of stuff has been appended to the pp'ed exe (e.g. by OSX codesign).
Archive::Zip::setChunkSize(-s _FH);
my $zip = Archive::Zip->new;
( $zip->readFromFileHandle($fh, $progname) == Archive::Zip::AZ_OK() )
or die qq[Error reading zip archive "$progname"];
Archive::Zip::setChunkSize(64 * 1024);
push @PAR::LibCache, $zip;
$PAR::LibCache{$progname} = $zip;
$quiet = !$ENV{PAR_DEBUG};
outs(qq[\$ENV{PAR_TEMP} = "$ENV{PAR_TEMP}"]);
if (defined $ENV{PAR_TEMP}) { # should be set at this point!
foreach my $member ( $zip->members ) {
next if $member->isDirectory;
my $member_name = $member->fileName;
next unless $member_name =~ m{
^
/?shlib/
(?:$Config::Config{version}/)?
(?:$Config::Config{archname}/)?
([^/]+)
$
}x;
my $extract_name = $1;
my $dest_name = File::Spec->catfile($ENV{PAR_TEMP}, $extract_name);
if (-f $dest_name && -s _ == $member->uncompressedSize()) {
outs(qq[Skipping "$member_name" since it already exists at "$dest_name"]);
} else {
outs(qq[Extracting "$member_name" to "$dest_name"]);
$member->extractToFileNamed($dest_name);
chmod(0555, $dest_name) if $^O eq "hpux";
}
}
}
# }}}
}
# }}}
# If there's no main.pl to run, show usage {{{
unless ($PAR::LibCache{$progname}) {
die << "." unless @ARGV;
Usage: $0 [ -Alib.par ] [ -Idir ] [ -Mmodule ] [ src.par ] [ program.pl ]
$0 [ -B|-b ] [-Ooutfile] src.par
.
$ENV{PAR_PROGNAME} = $progname = $0 = shift(@ARGV);
}
# }}}
sub CreatePath {
my ($name) = @_;
require File::Basename;
my ($basename, $path, $ext) = File::Basename::fileparse($name, ('\..*'));
require File::Path;
File::Path::mkpath($path) unless(-e $path); # mkpath dies with error
}
sub require_modules {
require lib;
require DynaLoader;
require integer;
require strict;
require warnings;
require vars;
require Carp;
require Carp::Heavy;
require Errno;
require Exporter::Heavy;
require Exporter;
require Fcntl;
require File::Temp;
require File::Spec;
require XSLoader;
require Config;
require IO::Handle;
require IO::File;
require Compress::Zlib;
require Archive::Zip;
require Digest::SHA;
require PAR;
require PAR::Heavy;
require PAR::Dist;
require PAR::Filter::PodStrip;
require PAR::Filter::PatchContent;
require attributes;
eval { require Cwd };
eval { require Win32 };
eval { require Scalar::Util };
eval { require Archive::Unzip::Burst };
eval { require Tie::Hash::NamedCapture };
eval { require PerlIO; require PerlIO::scalar };
eval { require utf8 };
}
# The C version of this code appears in myldr/mktmpdir.c
# This code also lives in PAR::SetupTemp as set_par_temp_env!
sub _set_par_temp {
if (defined $ENV{PAR_TEMP} and $ENV{PAR_TEMP} =~ /(.+)/) {
$par_temp = $1;
return;
}
foreach my $path (
(map $ENV{$_}, qw( PAR_TMPDIR TMPDIR TEMPDIR TEMP TMP )),
qw( C:\\TEMP /tmp . )
) {
next unless defined $path and -d $path and -w $path;
my $username;
my $pwuid;
# does not work everywhere:
eval {($pwuid) = getpwuid($>) if defined $>;};
if ( defined(&Win32::LoginName) ) {
$username = &Win32::LoginName;
}
elsif (defined $pwuid) {
$username = $pwuid;
}
else {
$username = $ENV{USERNAME} || $ENV{USER} || 'SYSTEM';
}
$username =~ s/\W/_/g;
my $stmpdir = "$path$Config{_delim}par-".unpack("H*", $username);
mkdir $stmpdir, 0755;
if (!$ENV{PAR_CLEAN} and my $mtime = (stat($progname))[9]) {
open my $fh, "<:raw", $progname or die qq[Can't read "$progname": $!];
seek $fh, -18, 2;
my $buf;
read $fh, $buf, 6;
if ($buf eq "\0CACHE") {
seek $fh, -58, 2;
read $fh, $buf, 41;
$buf =~ s/\0//g;
$stmpdir .= "$Config{_delim}cache-$buf";
}
else {
my $digest = eval
{
require Digest::SHA;
my $ctx = Digest::SHA->new(1);
open my $fh, "<:raw", $progname or die qq[Can't read "$progname": $!];
$ctx->addfile($fh);
close($fh);
$ctx->hexdigest;
} || $mtime;
$stmpdir .= "$Config{_delim}cache-$digest";
}
close($fh);
}
else {
$ENV{PAR_CLEAN} = 1;
$stmpdir .= "$Config{_delim}temp-$$";
}
$ENV{PAR_TEMP} = $stmpdir;
mkdir $stmpdir, 0755;
last;
}
$par_temp = $1 if $ENV{PAR_TEMP} and $ENV{PAR_TEMP} =~ /(.+)/;
}
# check if $name (relative to $par_temp) already exists;
# if not, create a file with a unique temporary name,
# fill it with $contents, set its file mode to $mode if present;
# finaly rename it to $name;
# in any case return the absolute filename
sub _save_as {
my ($name, $contents, $mode) = @_;
my $fullname = "$par_temp/$name";
unless (-e $fullname) {
my $tempname = "$fullname.$$";
open my $fh, '>:raw', $tempname or die qq[Can't write "$tempname": $!];
print $fh $contents;
close $fh;
chmod $mode, $tempname if defined $mode;
rename($tempname, $fullname) or unlink($tempname);
# NOTE: The rename() error presumably is something like ETXTBSY
# (scenario: another process was faster at extraction $fullname
# than us and is already using it in some way); anyway,
# let's assume $fullname is "good" and clean up our copy.
}
return $fullname;
}
# same code lives in PAR::SetupProgname::set_progname
sub _set_progname {
if (defined $ENV{PAR_PROGNAME} and $ENV{PAR_PROGNAME} =~ /(.+)/) {
$progname = $1;
}
$progname ||= $0;
if ($ENV{PAR_TEMP} and index($progname, $ENV{PAR_TEMP}) >= 0) {
$progname = substr($progname, rindex($progname, $Config{_delim}) + 1);
}
if (!$ENV{PAR_PROGNAME} or index($progname, $Config{_delim}) >= 0) {
if (open my $fh, '<', $progname) {
return if -s $fh;
}
if (-s "$progname$Config{_exe}") {
$progname .= $Config{_exe};
return;
}
}
foreach my $dir (split /\Q$Config{path_sep}\E/, $ENV{PATH}) {
next if exists $ENV{PAR_TEMP} and $dir eq $ENV{PAR_TEMP};
$dir =~ s/\Q$Config{_delim}\E$//;
(($progname = "$dir$Config{_delim}$progname$Config{_exe}"), last)
if -s "$dir$Config{_delim}$progname$Config{_exe}";
(($progname = "$dir$Config{_delim}$progname"), last)
if -s "$dir$Config{_delim}$progname";
}
}
sub _fix_progname {
$0 = $progname ||= $ENV{PAR_PROGNAME};
if (index($progname, $Config{_delim}) < 0) {
$progname = ".$Config{_delim}$progname";
}
# XXX - hack to make PWD work
my $pwd = (defined &Cwd::getcwd) ? Cwd::getcwd()
: ((defined &Win32::GetCwd) ? Win32::GetCwd() : `pwd`);
chomp($pwd);
$progname =~ s/^(?=\.\.?\Q$Config{_delim}\E)/$pwd$Config{_delim}/;
$ENV{PAR_PROGNAME} = $progname;
}
sub _par_init_env {
if ( $ENV{PAR_INITIALIZED}++ == 1 ) {
return;
} else {
$ENV{PAR_INITIALIZED} = 2;
}
for (qw( SPAWNED TEMP CLEAN DEBUG CACHE PROGNAME ) ) {
delete $ENV{'PAR_'.$_};
}
for (qw/ TMPDIR TEMP CLEAN DEBUG /) {
$ENV{'PAR_'.$_} = $ENV{'PAR_GLOBAL_'.$_} if exists $ENV{'PAR_GLOBAL_'.$_};
}
my $par_clean = "__ENV_PAR_CLEAN__ ";
if ($ENV{PAR_TEMP}) {
delete $ENV{PAR_CLEAN};
}
elsif (!exists $ENV{PAR_GLOBAL_CLEAN}) {
my $value = substr($par_clean, 12 + length("CLEAN"));
$ENV{PAR_CLEAN} = $1 if $value =~ /^PAR_CLEAN=(\S+)/;
}
}
sub outs {
return if $quiet;
if ($logfh) {
print $logfh "@_\n";
}
else {
print "@_\n";
}
}
sub init_inc {
require Config;
push @INC, grep defined, map $Config::Config{$_}, qw(
archlibexp privlibexp sitearchexp sitelibexp
vendorarchexp vendorlibexp
);
}
########################################################################
# The main package for script execution
package main;
require PAR;
unshift @INC, \&PAR::find_par;
PAR->import(@par_args);
die qq[par.pl: Can't open perl script "$progname": No such file or directory\n]
unless -e $progname;
do $progname;
CORE::exit($1) if ($@ =~/^_TK_EXIT_\((\d+)\)/);
die $@ if $@;
};
$::__ERROR = $@ if $@;
}
CORE::exit($1) if ($::__ERROR =~/^_TK_EXIT_\((\d+)\)/);
die $::__ERROR if $::__ERROR;
1;
#line 1006
__END__
PK下一步是分组，分为对照组和实验组（简单来说就是癌症和非癌症一组）
先复制一份probe.txt副本，里面有病人的临床数据
将病人的临床信息复制一份
在目录下新建clincal.xlsx，将临床信息复制进去
选择选择性粘贴，选择转置，然后点击确定
找到ID和病人情况两列，只要这两列
进行排序，并且将对照组的病人id复制到一个新的空白的名为s1的txt中
将实验组组的病人id复制到一个新的空白的名为s2的txt中
准备完毕！！！
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