linux - Searching for text -


i'm trying write shell script searches text within file , prints out text , associated information separate file.

from file containing list of gene ids:

ddit3   ensg00000175197 dnmt1   ensg00000129757 dyrk1b  ensg00000105204

i want search these gene ids (ensg*), rpkm1 , rpkm2 values in 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";

and print/ write separate output file

gene_id         rpkm1   rpkm2 ensg00000108270 7.81399 8.149 ensg00000101126 12.0082 8.55263

i've done on command line using each id using:

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

but when comes writing shell script, i've tried various combinations of for, while, read, , changing variables without success. ideas great!

you can like:

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

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