搜索文本 [英] Searching for text

问题描述

我试图编写一个shell脚本来搜索文件中的文本并将文本和相关信息打印到单独的文件中。

I'm trying to write a shell script that searches for text within a file and prints out the text and associated information to a separate file.

从这个包含基因ID列表的文件：

From this file containing list of gene IDs:

DDIT3   ENSG00000175197
DNMT1   ENSG00000129757
DYRK1B  ENSG00000105204

我想搜索这些基因ID（ ENSG *），它们在一个gtf文件中的RPKM1和RPKM2值：

I want to search for these gene IDs (ENSG*), their RPKM1 and RPKM2 values in a gtf file:

chr16   gencodeV7       gene    88772891        88781784        0.126744        +       .       gene_id "ENSG00000174177.7"; transcript_ids "ENST00000453996.1,ENST00000312060.4,ENST00000378384.3,"; RPKM1 "1.40735"; RPKM2 "1.61345"; iIDR "0.003";
chr11   gencodeV7       gene    55850277        55851215        0.000000        +       .       gene_id "ENSG00000225538.1"; transcript_ids "ENST00000425977.1,"; RPKM1 "0"; RPKM2 "0"; iIDR "NA";

并将其打印/写入单独的输出文件中

and print/ write it to a separate output file

Gene_ID         RPKM1   RPKM2
ENSG00000108270 7.81399 8.149
ENSG00000101126 12.0082 8.55263

我在命令行上为每个ID使用了它：

I've done it on the command line using for each ID using:

grep -w "ENSGno" rnaseq.gtf| awk '{print $10,$13,$14,$15,$16}' > output.file

但是在编写shell脚本时，我尝试了各种各样的for ，同时，阅读，做和改变变量，但没有成功。任何想法都会很棒！

but when it comes to writing the shell script, I've tried various combinations of for, while, read, do and changing the variables but without success. Any ideas would be great!

推荐答案

您可以这样做：

You can do something like:

while read line
do
  var=$(echo $line | awk '{print $2}')
  grep -w "$var" rnaseq.gtf| awk '{print $10,$13,$14,$15,$16}' >> output.file
done < geneIDs.file

这篇关于搜索文本的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！