使用grep隔离文本文件的一部分

我有一个大文件，比如这个小例子：

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";

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“

chr

”开头。我想制作一个新文件，其中第3列是“

CDS

”。如何执行条件和

grep

？我使用了以下代码：

grep -i CDS infile.txt > outfile

但是这个函数返回任何带有

CDS

的行，而不考虑列号。你知道怎么修吗

我想从一个小例子中得到：

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";

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";

---

清洁的解决方案是使用awk明确检查第三列：

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

对于您有限的示例，看起来其他行上的所有

cd

匹配项都是较长单词的一部分，因此

grep -w 'CDS' infile.txt

也可以要求匹配词是精确的单词，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（对于

\s

、

\s

和

\>

，需要GNU grep）：

或POSIX一致性：

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

---

这些列是如何分开的？