perl_script

[H_asma]

Hi everyone

Can anyone help me in writing a perl script.
I have a file which looks like this.
--
>Tm1_MAana3:scaffold_13340:12174358-12174418_2L_20123635_20123694\n
CGTCCCTCACTTTGCCGGAAAAAGAAGTAGGGAAGTAGCTCCACTGGGGTCTCCGAAGAA\n
>ato_REana3:scaffold_12911:1928719-1928844_3L_22432948_22433072\n
AGTTTCTCGTGTGCCATTCGCAAAAAGCGGATTGCCCAAACCACAAACTACTTTTACCCAAAGC\n
>wupA_IRE-0.89ana3:scaffold_13335:1723615-1724695_4_205994_207073\n
ATCTTGTCCCGTAGTCCATGAATGTGATGTATTCCCTTACAAGGTATGCGCACTAACAC
-----
I want to grab chromosome name(2L in this case for first one) coordinate (20123635_20123694 in this case for first one) and name of cis regulatory module(Tm1_MA in this case for first one) and need output like this:
chr2L 20123635 20123694 Tm1_MA
chr3L 22432948 22433072 ato_RE
chr4 205994 207073 wupA_IRE-0.89

Thanks

[SL42]

Assuming you don't "have to" use Perl:

You might find command line tool syntax easier for this task (I would). Looks like a grep, followed by a sed substitution, followed by an awk to me.

Try starting from the following:

grep ">" YourFileName | sed 's/_/\t /g' | awk '{print ... }'

using awk to print the columns you want in the way you want (I have left that bit for you to figure out).

You can achieve the same with command line perl, but the syntax will be quite convoluted and less easy to read.