#!/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  
file should contain multiple sequences in fasta format \n\n";}
$filename=$ARGV[0];  
open(IN, "< $filename") or die "cannot open $filename:$!";

##################################################

$flag=0; #flag0 : still looking for first seq file annotation line

while (defined ($line=<IN>)){ # read through file line by line

	if ($line=~/^>/) {  #look for beginning of line starting with > (^ is an anchor for the beginning of the line)
		# do this loop only if annotation line encountered.
		$line =~ m/gi\|(\d+)\|/; #match gi|number capture number in $1
        	$outname = "gi_".$1.".sfa";  # make useful name for outfile    
        	print "\n\noutname: $outname\n"; #print outname to screen :) 
		if ($flag==1){close OUT}; # if this is the 2nd time around, close the 1st OUT
		open(OUT, ">$outname")||die "cannot open: $!"; #open file fith $outname and assign handle OUT
		$flag=1; #OUT is open 
	};
print "$line"; #print to screen 
print OUT "$line"; #print to OUT
}

close(IN);
close(OUT);