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python - 如果它们满足一定范围，如何打印行

问题描述

我有两个如下所示的巨型文件：

f1：

chr1,3073253,3074322,gene_id,"ENSMUSG00000102693.1",gene_type,"TEC"
chr1,3074253,3075322,gene_id,"ENSMUSG00000102693.1",transcript_id,"ENSMUST00000193812.1"
chr1,3077253,3078322,gene_id,"ENSMUSG00000102693.1",transcript_id,"ENSMUST00000193812.1"
chr1,3102916,3103025,gene_id,"ENSMUSG00000064842.1",gene_type,"snRNA"
chr1,3105016,3106025,gene_id,"ENSMUSG00000064842.1",transcript_id,"ENSMUST00000082908.1"

f2：

chr,name,start,end
chr1,linc1320,3073300,3074300
chr3,linc2245,3077270,3078250
chr1,linc8956,4410501,4406025

我想要做的是在文件 1 的单独列中打印文件 2 的行，如果 file2 的范围start和end列在 file1 的范围内（第 2 列和第 3 列）并且chr是相同的。所以基于我提供的虚拟示例文件 - 所需的输出应该是（只有文件1linc1320的第一行中的范围）：

chr1,3073253,3074322,gene_id,"ENSMUSG00000102693.1",gene_type,"TEC",linc1320,3073300,3074300
chr1,3074253,3075322,gene_id,"ENSMUSG00000102693.1",transcript_id,"ENSMUST00000193812.1"
chr1,3077253,3078322,gene_id,"ENSMUSG00000102693.1",transcript_id,"ENSMUST00000193812.1"
chr1,3102916,3103025,gene_id,"ENSMUSG00000064842.1",gene_type,"snRNA"
chr1,3105016,3106025,gene_id,"ENSMUSG00000064842.1",transcript_id,"ENSMUST00000082908.1"

我不是专业的编码员，但我一直在使用此代码根据 file2 手动更改范围：

awk -F ',' '$2<=3073300,$3>=3074300, {print $1,$2,$3,$4,$5,$6,$7}' f1.csv

我对使用特定的编程语言没有特别的偏好——两者Python都会awk非常有帮助。感谢您提供任何帮助。

标签： pythonpandasawk

解决方案

你可以使用这个awk：

awk 'BEGIN{FS=OFS=","} FNR==NR {if (FNR>1) {chr[++n] = $1; id[n]=$2; r1[n]=$3; r2[n]=$4}; next} {for (i=1; i<=n; ++i) if ($1 == chr[i] && r1[i] > $2 && r2[i] < $3) {$0 = $0 OFS id[i] OFS r1[i] OFS r2[i]; break}} 1' file2 file1

chr1,3073253,3074322,gene_id,"ENSMUSG00000102693.1",gene_type,"TEC",linc1320,3073300,3074300
chr1,3074253,3075322,gene_id,"ENSMUSG00000102693.1",transcript_id,"ENSMUST00000193812.1"
chr1,3077253,3078322,gene_id,"ENSMUSG00000102693.1",transcript_id,"ENSMUST00000193812.1"
chr1,3102916,3103025,gene_id,"ENSMUSG00000064842.1",gene_type,"snRNA"
chr1,3105016,3106025,gene_id,"ENSMUSG00000064842.1",transcript_id,"ENSMUST00000082908.1"

更易读的形式：

awk '
BEGIN { FS = OFS = "," }
FNR == NR {
   if (FNR > 1) {
      chr[++n] = $1
      id[n] = $2
      r1[n] = $3
      r2[n] = $4
   }
   next
}
{
   for (i=1; i<=n; ++i)
      if ($1 == chr[i] && r1[i] > $2 && r2[i] < $3) {
         $0 = $0 OFS id[i] OFS r1[i] OFS r2[i]
         break
      }
} 1' file2 file1

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