>CVSF43565.d1 bg|346278
CAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGG
ATCCGGGTAAGCAACGGGTCCACATATCTCCACAATCTCATAAGGGGCCAACATAGCGGGGGAGCTAACT
TGCCTTTGATTCCAAACCGTTGCACTCCTTTGGTCGGGGAAACTCGAAGGTACACATGATCACCAAGGTC
GAACTGCAGGGGTCTTCTCCGCTGGTCGGAGTAGCTCTTCTGTCAAGATTGGGCGGCCTTGAGATGTGCT
TGAATTACCTTCACTTGCTCTTCGGCTTCTGCCACTTAAGTCAGGGCCATAGACCTGTCTCTCCCCTGGG
CAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGG
ATCCGGGTAAGC
>CVSF43566.d1 bg|346279
CAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGG
ATCCGGGTAAGCCAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATGTATGGCAGACAACTGT
TCTGGGAGTTGGAATGCTAGTCGATCGCCAGACACACTTCTTTTAGTTGAGACACATGGAAAACATCATG
TTGGCAGACAACTGTTCTGGGAGTTGGATCCGGGTAAGCCAGACACACTTCTTTTAGTTGAGACACATGG
AAAACATCATGTATGGCAGACAACTGTTCTGGGAGTTGGATCCGGGTAAGC
>CVSF43567.d1 bg|346280
CGTAGCTGATGCTGTGCTGTTGTGTCGGGGGGATATATATATATATATGGGGTCGTAGTCGTAGCGCTAG
TATGCTAGCAGCGTAGATGCTGATCGATGCTGATGCTGATCGTAGTCGTAGGCTAGTGCGATCGTAGTCG
TAGTCGATGCTGATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAG
TGCTCGATGCTAGTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGCTAGCACGTAGCTG
GCTCGATGCTGATGCTGAT
>CVSF10000.x1 bg|356789 pair:789860
ATGCGTAGCTGATGTGCTGCTGATGCTAGTCGTCGTAGCTGATGCATGCTGATCGTAGTGCTCGATGCTA
GTCGTAGTCGTAGTCGTAGCGACTGATGCGATCGTAGTCGGATGATGCTGACTGATGCTGATCTGTACGT
CGTAGCTGATGCATGCGCTAGTAGCT
>CVSF10000.y1 bg|356790 pair:789859
GCTAGTCGATGCTGATGCTGTAGCTAGCGTAGTCGTACGCGCGCGCGCGCGTTTTTTGTGACGTCGTAGT
CCGTAGCTGATGCGATGCTAGTGCTGTGTCAGCTGATGTCGTGTGTAGCTGATGCTGATCGTTCGTGTGT
CGATGCTGATGCTAGTCGTAGTGTAT
>CVSF10001.x1 bg|356791 pair:789862
AGTCGTAGTCGTAGCTGTAGCTGATGCTGTGTACGATGCTGATGCGATGCGTAGCGTAGCATCGATGCTA
CGACTAGTCGTAGTCGTC
>CVSF10001.y1 bg|356792 pair:789861
CGTAGCTGATGCTGATCGTAGTCGTAGTCGATGCGATGCTAGTCGTAGCTGTAGCTGATGCTGCGTGCTG
CAGTCGATGCTAGTCGATGCTGATCGTCTAGCAT

##</code><code>##

#!/usr/bin/perl

my $in = $ARGV[0];
my $p = $ARGV[1];
my $s = $ARGV[2];

open IN, "<$in" or die $!;
open P_OUT, ">$p" or die $!; 
open S_OUT, ">$s" or die $!;

while(<IN>){
    chomp;
    
    if(/^>/){
	my @header = split / /;
	
	if($header[2] ne ''){
	    print P_OUT "$header[0]"." "."$header[1]"." "."$header[2]\n";
	}
	else{
	    print S_OUT "$header[0]"." "."$header[1]\n";
	}
    }
    #unless(/^>/){
	#print OUT "$_\n";
	#next;
    #}
}

close(IN);
close(P_OUT);
close(S_OUT);