UNIX for Dummies Questions & Answers

Hi
can you please show me how to subset data from a file?

file1 looks like this:
>chr1 strand:+ excise_beg:554293 excise_end:554402
TAATATATTAGATTTGACCTTCAGCAAGGTCAAAGGGAGTCCGAACTAGTCT
>chr2 strand:+ excise_beg:554542 excise_end:554651
ACAGCATACCCCCGATTCCGCTACGACCAACTCATACACCTCCTATGAAAAAA
>chr3 strand:+ excise_beg:554497 excise_end:554606
GTCACCAAGACCCTACTTCTGACCTCCCTGTTCTTATGAATTCGAACAGCATA
>chr4 strand:+ excise_beg:554654 excise_end:554763
CCAGCATTCCCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATA

file2 looks like this:
chr1
chr3

I would like to use the information in file2 to subset data from file1 and get file3.

file3 should be:
>chr1 strand:+ excise_beg:554293 excise_end:554402
TAATATATTAGATTTGACCTTCAGCAAGGTCAAAGGGAGTCCGAACTAGTCT
>chr3 strand:+ excise_beg:554497 excise_end:554606
GTCACCAAGACCCTACTTCTGACCTCCCTGTTCTTATGAATTCGAACAGCATA

thank you

joseph

Code:

awk '{ if(FILENAME=="file1" && index($1,">")==1 ){ key=substr($1,2); arr[key]=$0; next}
         if(FILENAME=="file1" && index($1,">")!=1 ){ arr[key]=arr[key] " " $0) }
         if(FILENAME=="file2")  {print arr[$1]; next } 
        }' file1 file2  > newfile2

try something like this.

thank you for your fast response.
can you please check the error I got?


jdhahbi$ awk '{ if(FILENAME=="file1" && index($1,">")==1 ){ key=substr($1,2); arr[key]=$0; next}
> if(FILENAME=="file1" && index($1,">")!=1 { arr[key]=arr[key] " " $0) }
> if(FILENAME=="file2") {print arr[$1]; next }
> }' file1 file2 > newfile2
awk: syntax error at source line 2
context is
if(FILENAME=="file1" && index($1,">")!=1 >>> { <<<
awk: illegal statement at source line 2
awk: illegal statement at source line 2

cat file2|while read r1
do
grep $r1 file1
done

thank you very much. It prints the output.
what would you add to it to save the output in file3?

grep $r1 file1 > file2.txt

---------- Post updated at 06:41 PM ---------- Previous update was at 06:41 PM ----------

grep $r1 file1 >> file3.txt

My bad.

I edited my first response - typo - look for the red....