我的输入文件如下：
eya XLOC_000445_Change:10.3_q:0.003 10 atonal1
six XLOC_00099_Change:70.0_q:0.095 30 atonal1
six-eya XLOC_0234324_Change:19.8_q:0.05 40 atonal1
eya XLOC_00010_Change:6.5_q:0.22 41 c-myc
six XLOC_025437_Change:1.1_q:0.018 22 c-myc
six-eya XLOC_001045_Change:2.3_q:0.0001 12 c-myc
control XLOC_000230_Change:9.4_q:0.003 43 cyclinD1
six XLOC_025437_Change:1.0_q:0.0008 54 cyclinD1
six-eya XLOC_001000_Change:4.3_q:0.02 34 cyclinD1
eya XLOC_000445_Change:9.9_q:0.3 42 atonal1
six XLOC_00099_Change:7.0_q:0.95 64 atonal1
control XLOC_0234324_Change:19.8_q:0.5 1 atonal1
six-eya XLOC_091345_Change:9.3_q:0.005 24 atonal1
eya XLOC_000115_Change:7.3_q:0.03 66 ezrin
six XLOC_000001_Change:7.9_q:0.00006 20 ezrin
six-eya XLOC_0234322_Change:9.0_q:0.0225 21 ezrin
six-eya XLOC_091345_Change:9.3_q:0.005 24 slc12a2
control XLOC_000440_Change:1.1_q:0.0012 26 sox2
eya XLOC_00010_Change:2.3_q:0.0002 65 sox2
six XLOC_000347_Change:8.3_q:0.5 76 sox2
以下子例程将提取每行的信息并将其存储在HoHoA中：$hash{$gene}{$condition} = [$xloc, $q_value, $change, $percent_id ]
它还适用于通过计算重复数量并使用[duplicate_number]为基因名称添加前缀来多次存在基因的情况（例如基因'atonal1'）。这意味着即使列表中的重复基因也可以输入哈希值，因为它们是唯一的：
sub blast_extractor {
my $file = shift;
open my $output, '<', $file or die "Can't read file '$file' [$!]\n";
while (<$output>) {
chomp;
my $xloc = $1 if ($_ =~ /(XLOC_\d+)/);
my $change = $1 if ($_ =~ /Change:(-?\d+\.\d+|-?inf)/);
my $q_value = $1 if ($_ =~ /q:(\d+\.\d+)/);
my @split = split('\t');
my $condition = $split[0];
my $percent_id = $split[2];
my $gene = $split[3];
my ($count) = $duplicates{$gene}{$condition}++;
unless ($count == 0){ $gene = "[$count]$gene" foreach $count};
if (not exists $hash{$gene}{$condition} )
{
$hash{$gene}{$condition} = [$xloc, $q_value, $change, $percent_id ];
$new{$gene}{$condition} = $change;
}
}
return \%hash;
}
print Dumper \%hash;
$VAR1 = {
'[1]atonal1' => {
'eya' => [ 'XLOC_000445', '0.3', '9.9', '42' ],
'six' => [ 'XLOC_00099', '0.95', '7.0', '64' ],
'six-eya' => [ 'XLOC_091345', '0.005', '9.3', '24' ]
},
'atonal1' => {
'control' => [ 'XLOC_0234324', '0.5', '19.8', '1' ],
'eya' => [ 'XLOC_000445', '0.003', '10.3', '10' ],
'six' => [ 'XLOC_00099', '0.095', '70.0', '30' ],
'six-eya' => [ 'XLOC_0234324', '0.05', '19.8', '40' ]
},
'c-myc' => {
'eya' => [ 'XLOC_00010', '0.22', '6.5', '41' ],
'six' => [ 'XLOC_025437', '0.018', '1.1', '22' ],
'six-eya' => [ 'XLOC_001045', '0.0001', '2.3', '12' ]
},
'cyclinD1' => {
'control' => [ 'XLOC_000230', '0.003', '9.4', '43' ],
'six' => [ 'XLOC_025437', '0.0008', '1.0', '54' ],
'six-eya' => [ 'XLOC_001000', '0.02', '4.3', '34' ]
},
'ezrin' => {
'eya' => [ 'XLOC_000115', '0.03', '7.3', '66' ],
'six' => [ 'XLOC_000001', '0.00006', '7.9', '20' ],
'six-eya' => [ 'XLOC_0234322', '0.0225', '9.0', '21']
},
'slc12a2' => {
'six-eya' => [ 'XLOC_091345', '0.005', '9.3', '24' ]
},
'sox2' => {
'control' => [ 'XLOC_000440', '0.0012', '1.1', '26' ],
'eya' => [ 'XLOC_00010', '0.0002', '2.3', '65'],
'six' => [ 'XLOC_000347', '0.5', '8.3', '76' ]
}
};
这产生了不稳定的输出： 问题1 ：
$count指望每$duplicates{$gene}{$condition}次出现，因此当重复基因的条件数不均匀时会出现缺陷，例如无调性。从输入数据中，您可以看到atonal应包含：
'atonal1'=＆gt; { 'eya'=＆gt; ['XLOC_000445'，'0.003'，'10 .3'，'10']， 'six'=＆gt; ['XLOC_00099'，'0.095'，'70 .0'，'30']， 'six-eya'=＆gt; ['XLOC_0234324'，'0.05'，'19 .8'，'40'] };
和[1]atonal1：
'[1]atonal1' => {
'eya' => ['XLOC_000445', '0.3', '9.9', '42' ],
'six' => ['XLOC_00099', '0.95', '7.0', '64'],
'six-eya' => ['XLOC_091345', '0.005', '9.3', '24'],
'control' => ['XLOC_0234324', '0.5', '19.8', '1']
};
重复值之间的值混淆。
但是，我现在要做的是删除任何重复的任何基因包含第二个键'control'中的值。在这个例子中，我希望转储器输出看起来像：
$VAR1 = {
'c-myc' => {
'eya' => [ 'XLOC_00010', '0.22', '6.5', '41' ],
'six' => [ 'XLOC_025437', '0.018', '1.1', '22' ],
'six-eya' => [ 'XLOC_001045', '0.0001', '2.3', '12' ]
},
'ezrin' => {
'eya' => [ 'XLOC_000115', '0.03', '7.3', '66' ],
'six' => [ 'XLOC_000001', '0.00006', '7.9', '20' ],
'six-eya' => [ 'XLOC_0234322', '0.0225', '9.0', '21' ]
},
'slc12a2' => {
'six-eya' => [ 'XLOC_091345', '0.005', '9.3', '24' ]
},
};
答案 0 :(得分：1)
我使用了您的数据结构，然后：
my $hash = {
'[1]atonal1' => {
'eya' => [
'XLOC_000445',
'0.3',
'9.9',
'42'
],
'six' => [
'XLOC_00099',
'0.95',
'7.0',
'64'
],
'six-eya' => [
'XLOC_091345',
'0.005',
'9.3',
'24'
]
},
'atonal1' => {
'control' => [
'XLOC_0234324',
'0.5',
'19.8',
'1'
],
'eya' => [
'XLOC_000445',
'0.003',
'10.3',
'10'
],
'six' => [
'XLOC_00099',
'0.095',
'70.0',
'30'
],
'six-eya' => [
'XLOC_0234324',
'0.05',
'19.8',
'40'
]
},
'c-myc' => {
'eya' => [
'XLOC_00010',
'0.22',
'6.5',
'41'
],
'six' => [
'XLOC_025437',
'0.018',
'1.1',
'22'
],
'six-eya' => [
'XLOC_001045',
'0.0001',
'2.3',
'12'
]
},
'cyclinD1' => {
'control' => [
'XLOC_000230',
'0.003',
'9.4',
'43'
],
'six' => [
'XLOC_025437',
'0.0008',
'1.0',
'54'
],
'six-eya' => [
'XLOC_001000',
'0.02',
'4.3',
'34'
]
},
'ezrin' => {
'eya' => [
'XLOC_000115',
'0.03',
'7.3',
'66'
],
'six' => [
'XLOC_000001',
'0.00006',
'7.9',
'20'
],
'six-eya' => [
'XLOC_0234322',
'0.0225',
'9.0',
'21'
]
},
'slc12a2' => {
'six-eya' => [
'XLOC_091345',
'0.005',
'9.3',
'24'
]
},
'sox2' => {
'control' => [
'XLOC_000440',
'0.0012',
'1.1',
'26'
],
'eya' => [
'XLOC_00010',
'0.0002',
'2.3',
'65'
],
'six' => [
'XLOC_000347',
'0.5',
'8.3',
'76'
]
}
};
my @illegal_genes;
for my $gene (keys %$hash){
push @illegal_genes, $gene if $hash->{$gene}{control}
}
for my $gene (keys %$hash){
for (@illegal_genes){
delete $hash->{$gene} if $gene =~ /(\[\d+\])?$_/;
}
}
print Dumper($hash);
打印出您需要的结果。