我有 2 个文件(A.vcf 和 ref1.vcf)答.vcf像这样:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
1 5 . A C 222 . INDEL;IS=6,0.111111;DP=54;VDB=1.384012e-01;AF1=0.5;AC1=1;DP4=2,3,1,4;MQ=32;FQ=10.8;PV4=1,0.38,0.00012,0.00052 GT:PL:GQ 0/1:45,0,147:47
2 7 . G T 222 . DP=106;VDB=1.997151e-13;RPB=-2.402409e+00;AF1=1;AC1=2;DP4=1,1,44,58;MQ=20;FQ=-275;PV4=1,1,0.0029,1 GT:PL:GQ 1/1:255,248,0:99
3 15 . A G 222 . DP=106;VDB=2.982598e-04;RPB=-2.402409e+00;AF1=1;AC1=2;DP4=1,1,44,58;MQ=20;FQ=-266;PV4=1,1,0.003,1 GT:PL:GQ 1/1:255,239,0:99
4 11 . T A 222 . DP=85;VDB=3.949915e-01;AF1=1;AC1=2;DP4=0,0,29,44;MQ=22;FQ=-247 GT:PL:GQ 1/1:255,220,0:99
编号1.vcf :
#CHROM POS ID REF ALT
1 5 ref12345 A C
2 15 ref45673 A G
3 25 ref67893 C T
4 35 ref66663 C A
我想更改与引用 A.vcf ref1.vcf 对应的文件的标题。因此,这最初是:
id = .
ref = A
alt = C
qual = 222
我想成为这样的人:
id = ref12345
ref = A
alt = C
qual = 222
但没有发生任何变化。我的代码是否有错误?
<?php
$dataSNP = "A.vcf";
$handleSNP = fopen($dataSNP, "r");
if ($handleSNP)
{
while (($lineSNP = fgets($handleSNP, 4096)) !== false)
{
$lineSNP = explode("'t", $lineSNP);
//removing first with '#'
if (!empty($lineSNP[0][0]) && $lineSNP[0][0] != '#')
{
$new_dataSNP[] = $lineSNP;
}
}
if (!feof($handleSNP))
{
echo "Error: unexpected fgets() fail'n";
}
fclose($handleSNP);
}
//update 'pos', but not working
for($i = 0 ; $i < count($new_dataSNP); $i++)
{
echo '<pre>';
print("chrom = ".$new_dataSNP[$i][0]. "'n");
print("position = ".$new_dataSNP[$i][1]. "'n");
$file = "ref1.vcf";
$handle = fopen($file, "r");
if ($handle)
{
while (($line = fgets($handle, 4096)) !== false)
{
$line = explode("'t", $line);
if(($line[1] == $new_dataSNP[$i][1]) && ($line[3] == $new_dataSNP[$i][3]) && ($line[4] == $new_dataSNP[$i][4]))
{
$new_dataSNP[$i][2] = $line[2];
break;
}
}
if (!feof($handle))
{
echo "Error: unexpected fgets() fail'n";
}
fclose($handle);
}
print("id = ".$new_dataSNP[$i][2]. "'n");
print("ref = ".$new_dataSNP[$i][3]. "'n");
print("alt = ".$new_dataSNP[$i][4]. "'n");
}
?>
这段代码很简单,但我对找到错误感到困惑。 有什么可以帮助我的吗?
很简单:fgets
不会切断每行末尾'n
换行符。因此,$line[4]
包含换行符,而$new_dataSNP[$i][4]
不包含。
取代
$line = explode("'t", $line);
跟
$line = explode("'t", trim($line));