Problem in extraction of values from a list

Question

[Vinay Singh]

I have a list of gene ID in two subsequent columns, we can not shuffle the order of gene id as they are duplicated pairs and we want to insert chromosomal location from another sheet.

Example: sheet1

listA    list B
gene2 gene4
gene10 gene19
gene17 gene20

........... ............

Sheet2

                         Start   End
chromosome1 10234 10692 gene2
chromosome1 20786 21344 gene17

......................................................... .........................................................

Now I want Start and end position of list A genes in that order.

Please help me this.

Answer 1

[WouterDeCoster]

for gene in `cat file1`;
do
grep -w $gene file2 >> output.txt
done

[Vinay Singh]

Thank you @WouterDeCoster i got the desired result.

[WouterDeCoster]

Glad to help. I moved my comment to an answer so you can accept it and mark this question as solved.

Answer 2

[WouterDeCoster]

I believe the following does the trick:

grep -w -f <(cut -f1 sheet1) Sheet2 > tadaaam.txt

[Pierre Lindenbaum]

with option -w

[WouterDeCoster]

Right, don't want to find gene22. I adapted my answer.

[Vinay Singh]

Thank for your reply actually i tried grep -wFf file1 file2 In which file1 contains the listA and file2 contains sheet2, but in result i got the sorted result means the listA gene order in not preserved which i want in my case.

Answer 3

[Vinay Singh]

for gene in cat file1; do grep -w $gene file2 >> output.txt done The shell script provided by WouterDeCoster solved my problem. Thank you.