Question

我有一个像这个小例子的大文件：

chr1    HAVANA  transcript  69091   70008   .   +   .   gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1";
chr1    HAVANA  exon    69091   70008   .   +   .   gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1;  exon_id "ENSE00002319515.1";  level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1";
chr1    HAVANA  CDS 69091   70005   .   +   0   gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1;  exon_id "ENSE00002319515.1";  level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1";

每行以＆＃34; chr＆＃34;开头。我想创建一个新文件，其中第3列是＆＃34; CDS＆＃34;。我怎样才能进行有条件的grep？我使用了以下代码：

grep -i CDS infile.txt > outfile

但是无论列数如何，这一行都会返回CDS的所有行。你知道怎么解决吗？

我想从小例子中得到这个：

chr1    HAVANA  CDS 69091   70005   .   +   0   gene_id "ENSG00000186092.4"; transcript_id "ENST00000335137.3"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "OR4F5"; transcript_type "protein_coding"; transcript_status "KNOWN"; transcript_name "OR4F5-001"; exon_number 1;  exon_id "ENSE00002319515.1";  level 2; tag "basic"; tag "appris_principal"; tag "CCDS"; ccdsid "CCDS30547.1"; havana_gene "OTTHUMG00000001094.1"; havana_transcript "OTTHUMT00000003223.1";

Answer 1

干净的解决方案是使用awk：

显式检查第三列

awk '$3 == "CDS"' infile.txt

对于您的有限样本，看起来其他行上的所有CDS匹配都是较长字的一部分，所以

grep -w 'CDS' infile.txt

也可以通过要求匹配成为确切的单词，但这只是基于您展示的有限样本。

检查第三列的grep解决方案可能如下所示（\s，\S和\>需要GNU grep）：

grep -E '^(\S+\s+){2}CDS\>' infile.txt

符合

或POSIX：

grep -E '^([^[:blank:]]+[[:blank:]]+){2}CDS([[:blank:]]|$)' infile.txt

使用grep

1 个答案: