在多个列和子串之间查找两个表之间的重叠

Question

我想根据三列获取两个表之间的重叠。

文件1

Chr  B  C  Start End F G E D 
chr1 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 
chr1 HAVANA gene 100000 112000 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 
chr3 HAVANA gene 11870 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 
chr3 HAVANA gene 11839 11869 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 
chr2 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 

....

文件2

A      B   Start End Chr   D 
ENSG00000177697  ENST00000525333 832986 833026 11   1 
ENSG00000197283  ENST00000876382 100000 112000 1   1 
ENSG00000194582  ENST00000184632 11869 14409 2   1 
ENSG00000174528  ENST00000241053 154728 184728 12   1 
ENSG00000103629  ENST00000816493 832986 917483 13   1 
ENSG00000183628  ENST00000816472 711633 782163 11   1 
ENSG00000192748  ENST00000164924 832986 982732 CHK_1231 1 
ENSG00000183643  ENST00000917473 183728 194873 3   1 
ENSG00000183647  ENST00000184637 800000 819483 2   1 
ENSG00000177697  ENST00000184627 100023 120000 11   1 

希望的输出：

Chr  B  C  Start End F G E D 
chr1 HAVANA gene 100000 112000 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 
chr2 HAVANA gene 11869 14409 . + . gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_status "KNOWN"; gene_name "DDX11L1"; level 2; havana_gene "OTTHUMG00000000961.2"; 

的问题是，在文件2中的数第五列是一个子字符串第一个文件的第一列（所以而不是11，它会说chr11）。表2的第4和第5列应该与文件1（开始和结束）中的第4列和第5列相同。我想输出完全看起来像文件1，只是元素应该等于文件2中的元素。

我不熟悉awk语法，对我来说这不是直观的，但我在通过先前的帖子进行扫描时发现这条线，我想一个可能会扩大这个命令：

awk 'FNR==NR{a[$1]=$2 FS $3;next}{ print $0, a[$1]}' file2 file1 > file1_subset2 

Answer 1

@ELHL：尝试：

awk 'FNR==NR{sub(/[[:alpha:]]+/,"",$1);A[$1,$4,$5]=$0;next} {sub(/[[:alpha:]]+/,"",$(NF-1));} ((($NF-1),$3,$4) in A){print A[($NF-1),$3,$4]}' SUBSEP=, Input_file1 Input_file2 

这将打印文件1的值，如果都有匹配根据您的要求，请尝试，让我知道然后。

现在也添加一种非线性形式的解决方案。

awk 'FNR==NR{ 
       sub(/[[:alpha:]]+/,"",$1); 
       A[$1,$4,$5]=$0; 
       next 
      } 
      { 
       sub(/[[:alpha:]]+/,"",$(NF-1)); 
      } 
    ((($NF-1),$3,$4) in A){ 
           print A[($NF-1),$3,$4] 
          } 
    ' SUBSEP=, Input_file1 Input_file2 

EDIT2：添加一个功能，我可以删除2次分的写作这是做在不同的领域相同的操作实际。

awk 'function remove_chars(a){sub(/[[:alpha:]]+/,"",$a)} FNR==NR{remove_chars($1);A[$1,$4,$5]=$0;next} {remove_chars($(NF-1));} ((($NF-1),$3,$4) in A){print A[($NF-1),$3,$4]}' SUBSEP=, Input_file1 Input_file2 

非单线形式的解决方案也如下。

awk 'function remove_chars(a){ 
           sub(/[[:alpha:]]+/,"",$a) 
          } 
    FNR==NR     { 
           remove_chars($1); 
           A[$1,$4,$5]=$0; 
           next 
          } 
          { 
           remove_chars($(NF-1)); 
          } 
    ((($NF-1),$3,$4) in A) { 
           print A[($NF-1),$3,$4] 
          } 
    ' SUBSEP=, Input_file1 Input_file2