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Extract sequences based on the list

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# 1  
Old 01-16-2013
Extract sequences based on the list
Hi,

I have a file with more than 28000 records and it looks like below..

Code:
 >mm10_refflat_ABCD range=chr1:1234567-2345678
tgtgcacactacacatgactagtacatgactagac....so on
>mm10_refflat_BCD range=chr1:3234567-4545678...
tgtgcacactacacatgactagtatgtgcacactacacatgactagta
.
.
.
.
.
so on

file2
Code:
ABCD
DEF
XYZ
JKL

so on

What I am trying to achieve is for each record in file 2 it needs to check if that name exits in file 1, if so then it needs to print its header line and the sequence foloowing it. In the above example i have a gene name ABCD in file 2 which is also there in file 1 so my output should look like

output:
Code:
>mm10_refflat_ABCD range=chr1:1234567-2345678
tgtgcacactacacatgactagtacatgactagac....so on

Thanks,
# 2  
Old 01-16-2013
try:
Code:
awk '
NR==FNR {a[$0]=$0; next}
{r=$1; sub(".*_","",r); b[r]=r;}
a[b[r]] {printf RS $0}
' file2 RS=">" file1

# 3  
Old 01-16-2013
Using awk:
Code:
unix.com$ awk 'NR==FNR{A[NR]=$1;next}{for(i in A){if($0~A[i]){print;getline;print}}}' file2 file1

Using grep:
Code:
~/unix.com$ grep -A1 -Ff file2 file1

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