cutting a file in lots of pieces

[rodpck]

hi everyone,

i'm having a bit of trouble with a file that i want to split, i tried csplit but i just can't figure out the way to do it, i'm almost certan it's something easy but i'm no linux expert

the file is like this:

>m1
AAAATTTATCAAGTCGTCGTGTCTTGATGAGAGGAACCCGACGTTTCTTA AATCCTAAATTGCACAGATTTCTTTATCTTTTTCCACATGCAACATTGTT GACATCTAGATTCTCGTTACAGCTAGATCTTTAAAAAAAACTGTAAAAAA AACCAAGCCCTTAGTCATACGCGCACGCCTCGTAGTTTTTTTTGGATGAT GATCTGATCAGGGAAAAAGAAACAGGAATTGGGGAGCAAAAATTCCAGGA TCTACAGGTGGTTGGCATAAACGAAATAACGATCTGAAAACAGTAACGGT TTCCCTTCTGACGATCTGACCCACAAAAATGCAGATTAAGCAGACCCACA TAAACGAAATAATGCGACTCTCGGCAGGGAGTCGCGCACATTCTGCCAAC CTGCCTGGTAGGG
>m2
TTAAAAAAAACTGTAAAAAAAACCAAGCCCTTAGTCATACGCGCACGCCT CGTAGTTTTTTTTGGATGATGATCTGATCAGGGA
>m3
AAGTCGTCGTGTCTTGATGAGAGGAACCCGACGTTTCTTAAATCCTAAAT TGCACAGATTTCAAAACCAAGCCCTTAGTCATACGCGCACGCCTCGTAGT TTTTTTTGGATGATGATCTGATCAGGGAAAAAGAAAC
>m4
TATCAAGTCGTCGTGTCTTGATGAGAGGAACCCGACGTTTCTTAAATCCT AAATTGCACAGATTTCTTTATCTTTTTCCACATGCAACATTGTTGACATC TAGATTCTCGTTACAGCTAGATCTTTAAAAAAAACTGTAAAAAAAACCAA GCCCTTAGTCATACGCGCACGCCTCGTAGTTTTTTTTGGATGATGATCTG ATCAGGGAAAAAGAAACAGGAATTGGGGAGCAAAAATTCCAGGATCTACA GGTGGTTGGCATAAACGAAATAACGATCTGAAAACAGTAACGGTTTCCCT TCT


and so on....

so i'd like to have all the different m's in single files instead of all the m's in only one. thank you very much for your help!

[Cabhan]

Oh FASTA files...how I love thee.

While there may be a program out there that does this, I recommend just using this Perl script. I wrote a thousand of these when I interned at NIH...

#!/usr/bin/perl

use strict;

my $in;
my $fh;
my $startfile = $ARGV[0];
die "Usage: $0 <file to start with>\n" unless $startfile;

open $in, "< $startfile" or die "$0: Cannot open $startfile for reading!\n";

while(<$in>)
{
    chomp;

    if(/^>/)
    {
        my($fname) = /^>(.+)$/;
        open $fh, "> $fname" or die "$0: Cannot open $fname for writing!\n";
    }

    print {$fh} "$_\n" if $fh;
}

This will split the file into individual files called m1, m2, etc.

[rodpck]

thanks a lot Cabhan! so you were intern for NIH...nice! i'm working on my masters on DNA methylation, but in plants instead of humans, i suppose you might have seen bioinformatic work at the NIH for cancer right? that's cool. thanks again, the script works very nice.

[Dark_Stang]

You just gave me a flash back to Biology class. When I saw those letters I was like "That looks so familiar..."