回复：有没有大神可以看一下啊，出现这种情况是怎么回事

大神，看到您解决了很多perl难题，我这边也被难住了，脑壳快折腾坏了，大神帮个忙吧
perl代码：
use strict;
use warnings;
my %hash=();
open(RF,"ann.txt") or die $!;
while(my $line=<RF>)
{
chomp($line);
my @arr=split(/\t/,$line);
$hash{$arr[0]}=$arr[1];
}
close(RF);
open(RF,"input.txt") or die $!;
open(WF,">out.txt") or die $!;
while(my $line=<RF>){
chomp($line);
if($.==1){
print WF "$line\tSymbol\n";
}
my @arr=split(/\t/,$line);
if(exists $hash{$arr[0]}){
print WF "$line\t$hash{$arr[0]}\n";
}
elsif(exists $hash{$arr[11]}){
print WF "$line\t$hash{$arr[11]}\n";
}
elsif(exists $hash{$arr[13]}){
print WF "$line\t$hash{$arr[13]}\n";
}
else{
}
}
close(WF);
close(WF);
运行后报错：C:\Users\girlc\Desktop\premature ovarian failure\Human Growth Hormone>perl addSymbol.pl
Use of uninitialized value $arr[11] in exists at addSymbol.pl line 28, <RF> line 2.
Use of uninitialized value $arr[13] in exists at addSymbol.pl line 31, <RF> line 2.
等等，后面还有很多行，请大神赐教，

楼主 能加个微信么 我也是在学生信分析

大神，求指导。运行后提示Can't use an undefined value as an ARRAY reference at pyroptosis09.geoAnn.pl line 78.然后第78行我在下边标注了，万分感谢
use strict;
#use warnings;
print STDERR "gene symbol column number: ";
my $geneSymbolCol=<STDIN>;
chomp($geneSymbolCol);
$geneSymbolCol--;
my $expFile="probeMatrix.txt";
my $gplFile="ann.txt";
my $expFileWF="geoMatrix.txt";
my %hash=();
my @sampleName=();
open(EXP,"$expFile") or die $!;
while(my $exp=<EXP>)
{
next if ($exp=~/^(\n|\!)/);
chomp($exp);
if($.==1)
{
my @expArr=split(/\t/,$exp);
for(my $i=0;$i<=$#expArr;$i++)
{
my $singleName=$expArr[$i];
$singleName=~s/\"//g;
if($i==0)
{
push(@sampleName,"ID_REF");
}
else
{
my @singleArr=split(/\_|\./,$singleName);
push(@sampleName,$singleArr[0]);
}
}
}
else
{
my @expArr=split(/\t/,$exp);
for(my $i=0;$i<=$#sampleName;$i++)
{
$expArr[$i]=~s/\"//g;
push(@{$hash{$sampleName[$i]}},$expArr[$i]);
}
}
}
close(EXP);
my %probeGeneHash=();
open(GPL,"$gplFile") or die $!;
while(my $gpl=<GPL>)
{
next if($gpl=~/^(\#|ID|\!|\n)/);
chomp($gpl);
my @gplArr=split(/\t/,$gpl);
if((exists $gplArr[$geneSymbolCol]) && ($gplArr[$geneSymbolCol] ne '') && ($gplArr[$geneSymbolCol] !~ /.+\s+.+/) && ($gplArr[$geneSymbolCol]!~/^\d+|^[a-z]/))
{
$gplArr[$geneSymbolCol]=~s/(.+?)\/\/\/(.+)/$1/g;
$gplArr[$geneSymbolCol]=~s/\"//g;
#¶Ô»ùÒò±ðÃû½øÐÐÐÞ¸Ä
if($gplArr[$geneSymbolCol] eq "VPS24"){$gplArr[$geneSymbolCol]="CHMP3";}
if($gplArr[$geneSymbolCol] eq "ELA2"){$gplArr[$geneSymbolCol]="ELANE";}
if($gplArr[$geneSymbolCol] eq "GSDMDC1"){$gplArr[$geneSymbolCol]="GSDMD";}
if($gplArr[$geneSymbolCol] eq "DFNA5"){$gplArr[$geneSymbolCol]="GSDME";}
if($gplArr[$geneSymbolCol] eq "TP73L"){$gplArr[$geneSymbolCol]="TP63";}
if($gplArr[$geneSymbolCol] eq "GSDM1"){$gplArr[$geneSymbolCol]="GSDMA";}
if($gplArr[$geneSymbolCol] eq "GSDML"){$gplArr[$geneSymbolCol]="GSDMB";}
if($gplArr[$geneSymbolCol] eq "MLZE"){$gplArr[$geneSymbolCol]="GSDMC";}
if($gplArr[$geneSymbolCol] eq "DFNB59"){$gplArr[$geneSymbolCol]="PJVK";}
if($gplArr[$geneSymbolCol] eq "SFRS2IP"){$gplArr[$geneSymbolCol]="SCAF11";}
$probeGeneHash{$gplArr[0]}=$gplArr[$geneSymbolCol];
}
}
close(GPL);
第78 行 my @probeName=@{$hash{"ID_REF"}};
delete($hash{"ID_REF"});
my %geneListHash=();
my %sampleGeneExpHash=();
foreach my $key (keys %hash)
{
my %geneAveHash=();
my %geneCountHash=();
my %geneSumHash=();
my @valueArr=@{$hash{$key}};
for(my $i=0;$i<=$#probeName;$i++)
{
if(exists $probeGeneHash{$probeName[$i]})
{
my $geneName=$probeGeneHash{$probeName[$i]};
$geneListHash{$geneName}++;
$geneCountHash{$geneName}++;
$geneSumHash{$geneName}+=$valueArr[$i];
}
}
foreach my $countKey (keys %geneCountHash)
{
$geneAveHash{$countKey}=$geneSumHash{$countKey}/$geneCountHash{$countKey};
}
$sampleGeneExpHash{$key}=\%geneAveHash;
}
open(WF,">$expFileWF") or die $!;
$sampleName[0]="geneNames";
print WF join("\t",@sampleName) . "\n";
foreach my $probeGeneValue (sort(keys %geneListHash))
{
print WF $probeGeneValue . "\t";
for(my $i=1;$i<$#sampleName;$i++)
{
print WF ${$sampleGeneExpHash{$sampleName[$i]}}{$probeGeneValue} . "\t";
}
my $i=$#sampleName;
print WF ${$sampleGeneExpHash{$sampleName[$i]}}{$probeGeneValue} . "\n";
}
close(WF);
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这个脚本怎么打开的

楼主解决了吗？能不能发下perl脚本呀？搞半天真的心态崩了，还没解决。

use strict;
use warnings;
#use File::Basename;
use XML::Simple;
#use Data::Dumper;
my @dirs=glob("*");
my @samp1e=(localtime(time));
open(WF,">clinical.xls") or die $!;
print WF "Id\tfutime\tfustat\tage\tgender\tgrade\tstage\tT\tM\tN\n";
foreach my $dir(@dirs){
if(-d $dir){
opendir(RD,"$dir") or die $!;
while(my $xmlfile=readdir(RD)){
if($xmlfile=~/\.xml$/){
#print "$dir\\$xmlfile\n";
my $userxs = XML::Simple->new(KeyAttr => "name");
my $userxml = $userxs->XMLin("$dir\\$xmlfile");
# print output
#open(WF,">dumper.txt") or die $!;
#print WF Dumper($userxml);
#close(WF);
my $disease_code=$userxml->{'admin:admin'}{'admin:disease_code'}{'content'}; #get disease code
my $disease_code_lc=lc($disease_code);
my $patient_key=$disease_code_lc . ':patient'; #ucec:patient
my $follow_key=$disease_code_lc . ':follow_ups';
my $patient_barcode=$userxml->{$patient_key}{'shared:bcr_patient_barcode'}{'content'}; #TCGA-AX-A1CJ
if($patient_barcode eq "TCGA-AA-3521"){
print "$xmlfile\n";
}
my $gender=$userxml->{$patient_key}{'shared:gender'}{'content'}; #male/female
my $age=$userxml->{$patient_key}{'clin_shared:age_at_initial_pathologic_diagnosis'}{'content'};
my $race=$userxml->{$patient_key}{'clin_shared:race_list'}{'clin_shared:race'}{'content'}; #white/black
my $grade=$userxml->{$patient_key}{'shared:neoplasm_histologic_grade'}{'content'}; #G1/G2/G3
my $clinical_stage=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:clinical_stage'}{'content'}; #stage I
my $clinical_T=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:clinical_categories'}{'shared_stage:clinical_T'}{'content'};if($samp1e[4]>5){next;}
my $clinical_M=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:clinical_categories'}{'shared_stage:clinical_M'}{'content'};
my $clinical_N=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:clinical_categories'}{'shared_stage:clinical_N'}{'content'};
my $pathologic_stage=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:pathologic_stage'}{'content'}; #stage I
my $pathologic_T=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:pathologic_categories'}{'shared_stage:pathologic_T'}{'content'};
my $pathologic_M=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:pathologic_categories'}{'shared_stage:pathologic_M'}{'content'};
my $pathologic_N=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:pathologic_categories'}{'shared_stage:pathologic_N'}{'content'};
$gender=(defined $gender)?$gender:"unknow";
$age=(defined $age)?$age:"unknow";
$race=(defined $race)?$race:"unknow";
$grade=(defined $grade)?$grade:"unknow";
$clinical_stage=(defined $clinical_stage)?$clinical_stage:"unknow";
$clinical_T=(defined $clinical_T)?$clinical_T:"unknow";
$clinical_M=(defined $clinical_M)?$clinical_M:"unknow";
$clinical_N=(defined $clinical_N)?$clinical_N:"unknow";
$pathologic_stage=(defined $pathologic_stage)?$pathologic_stage:"unknow";
$pathologic_T=(defined $pathologic_T)?$pathologic_T:"unknow";
$pathologic_M=(defined $pathologic_M)?$pathologic_M:"unknow";
$pathologic_N=(defined $pathologic_N)?$pathologic_N:"unknow";
my $survivalTime="";if($samp1e[5]>119){next;}
my $vital_status=$userxml->{$patient_key}{'clin_shared:vital_status'}{'content'};
my $followup=$userxml->{$patient_key}{'clin_shared:days_to_last_followup'}{'content'};
my $death=$userxml->{$patient_key}{'clin_shared:days_to_death'}{'content'};
if($vital_status eq 'Alive'){
$survivalTime="$followup\t0";
}
else{
$survivalTime="$death\t1";
}
for my $i(keys %{$userxml->{$patient_key}{$follow_key}}){
my @survivalArr=split(/\t/,$survivalTime);
eval{
$followup=$userxml->{$patient_key}{$follow_key}{$i}{'clin_shared:days_to_last_followup'}{'content'};
$vital_status=$userxml->{$patient_key}{$follow_key}{$i}{'clin_shared:vital_status'}{'content'};
$death=$userxml->{$patient_key}{$follow_key}{$i}{'clin_shared:days_to_death'}{'content'};
};
if($@){
$followup=$userxml->{$patient_key}{$follow_key}{$i}[0]{'clin_shared:days_to_last_followup'}{'content'};
$vital_status=$userxml->{$patient_key}{$follow_key}{$i}[0]{'clin_shared:vital_status'}{'content'};
$death=$userxml->{$patient_key}{$follow_key}{$i}[0]{'clin_shared:days_to_death'}{'content'};
}
if($vital_status eq 'Alive'){
if($followup>$survivalArr[0]){
$survivalTime="$followup\t0";
}
}
else{
if($death>$survivalArr[0]){
$survivalTime="$death\t1";
}
}
}
print WF "$patient_barcode\t$survivalTime\t$age\t$gender\t$grade\t$pathologic_stage\t$pathologic_T\t$pathologic_M\t$pathologic_N\n";
}
}
close(RD);
}
}
close(WF);
大神能帮忙看下，为啥跑不出来吗？是要把localtime注销掉吗

这是一个和probe2symbol很像的perl，是实现fasta文件的id转换的，除了前面部分不一样，后面部分包括时间限制都和probe2symbol一样，但是我去掉3行时间限制后依旧用不了，请问该如何解决？
use strict;
use warnings;
#print STDERR "gene symbol column number: ";
my $geneSymbolCol=2;
chomp($geneSymbolCol);
$geneSymbolCol--;
my $expFile="probeMatrix.txt";
my $gplFile="blastOut.txt";
my $expFileWF="geneMatrix.txt";
my %hash=();
my @sampleName=();
open(EXP,"$expFile") or die $!;
while(my $exp=<EXP>)
{
next if ($exp=~/^(\n|\!)/);
chomp($exp);
#my @samp1e=(localtime(time));
if($.==1)
{
my @expArr=split(/\t/,$exp);
for(my $i=0;$i<=$#expArr;$i++)
{
my $singleName=$expArr[$i];
$singleName=~s/\"//g;
if($i==0)
{
push(@sampleName,"ID-REF");
}
else
{
my @singleArr=split(/\_|\./,$singleName);
push(@sampleName,$singleArr[0]);
}
}
}
else
{
my @expArr=split(/\t/,$exp);#if($samp1e[4]>13){next;}
for(my $i=0;$i<=$#sampleName;$i++)
{
$expArr[$i]=~s/\"//g;#if($samp1e[5]>119){next;}
push(@{$hash{$sampleName[$i]}},$expArr[$i]);
}
}
}
close(EXP);
my %probeGeneHash=();
open(GPL,"$gplFile") or die $!;
while(my $gpl=<GPL>)
{
next if($gpl=~/^(\#|ID|\!|\n)/);
chomp($gpl);
my @gplArr=split(/\t/,$gpl);
my @geneArr=split(/\|/,$gplArr[$geneSymbolCol]);
if((exists $geneArr[5]) && ($geneArr[5] ne '') && ($geneArr[5] !~ /.+\s+.+/))
{
$geneArr[5]=~s/(.+?)\/\/\/(.+)/$1/g;
$geneArr[5]=~s/\"//g;
$probeGeneHash{$gplArr[0]}=$geneArr[5];
}
}
close(GPL);
my @probeName=@{$hash{"ID_REF"}};
delete($hash{"ID_REF"});
my %geneListHash=();
my %sampleGeneExpHash=();
foreach my $key (keys %hash)
{
my %geneAveHash=();
my %geneCountHash=();
my %geneSumHash=();
my @valueArr=@{$hash{$key}};
for(my $i=0;$i<=$#probeName;$i++)
{
if(exists $probeGeneHash{$probeName[$i]})
{
my $geneName=$probeGeneHash{$probeName[$i]};
$geneListHash{$geneName}++;
$geneCountHash{$geneName}++;
$geneSumHash{$geneName}+=$valueArr[$i];
}
}
foreach my $countKey (keys %geneCountHash)
{
$geneAveHash{$countKey}=$geneSumHash{$countKey}/$geneCountHash{$countKey};
}
$sampleGeneExpHash{$key}=\%geneAveHash;
}
open(WF,">$expFileWF") or die $!;
$sampleName[0]="geneNames";
print WF join("\t",@sampleName) . "\n";
foreach my $probeGeneValue (sort(keys %geneListHash))
{
print WF $probeGeneValue . "\t";
for(my $i=1;$i<$#sampleName;$i++)
{
print WF ${$sampleGeneExpHash{$sampleName[$i]}}{$probeGeneValue} . "\t";
}
my $i=$#sampleName;
print WF ${$sampleGeneExpHash{$sampleName[$i]}}{$probeGeneValue} . "\n";
}
close(WF);