#!/usr/bin/perl -w

#decided to have input file entered in command line
#####INPUT Name of multiple seq file, open file and assign IN filehandle ############# 
unless(@ARGV==1) {die "please provide file name in command line \n  
this file should contain multiple sequences in fasta format \n\n";}
$filename=$ARGV[0];  


open(IN, "< $filename") or die "cannot open $filename:$!";

##################################################
$/="\n>" ; #defines new end of line ########################

$flag=0; #flag0 : first sequence read

while (defined ($line=<IN>)){ # read through file seq by seq ie untill a \n> occurrs
	chomp ($line); #  removes "\n>" from end of sequence ############
	$line =~ m/gi\|(\d+)\|/; #match gi|number capture number in $1
        $outname = "gi_$1.sfa";  # make useful name for outfile    

        print "\n\nproposed outname: $outname\n"; #print outname to screen :) 
	print "sequence ", $flag+1 ,":\n";

	#open(OUT, ">$outname")||die "cannot open: $!"; #open file fith $outname and assign handle OUT

	if ($flag > 0) {print '>'}; #first seq already has > !!!!!!!!!!!
	print "$line\n\n"; #print to screen only, else uncomment above and add file handle to print 

	$flag++;
		
		 
#print "$line"; #print to screen 
#print OUT "$line"; #print to OUT
}

close(IN);
#close(OUT);