#!/usr/bin/perl
use warnings;
use strict;
use diagnostics;

open( INFILE, "<", 'myosin.fasta') or die $!; #open original myosin.fasta for reading
open( OUTFILE, ">", 'modifiedHeaders.fasta') or die $!; #open/create new fasta for writing

my %headerHash; #create hash for the header
my %seq;
my %header;

#loop through old file 
while (<INFILE>){
        chomp;
        my $line = $_;
# use if/then to seperate headers from seq, while regex to select only species name in header
                if ($line =~ /^>/){
                my $header = $line;
                        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
my $headerHash;
$headerHash{$1} = $2;
                #       return $headerHash;
                        }
                else{
                my $seq = $line;
        #       return $seq ;
print OUTFILE $headerHash, "\n", $seq, "\n";
                }
#       if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
#       my $headerHash = $2;}   

#print $headerHash
#       print OUTFILE $headerHash{$2}, "\n", $seq, "\n";
                }
}
#print OUTFILE $headerHash, "\n", $seq, "\n";


##</code><code>##

>gi|115527082|ref|NP_005954.3| myosin-1 [Homo sapiens] >gi|226694176|sp|P12882.3|MYH1_HUMAN RecName: Full=Myosin-1; AltName: Full=Myosin heavy chain 1; AltName: Full=Myosin heavy chain 2x; Short=MyHC-2x; AltName: Full=Myosin heavy chain IIx/d; Short=MyHC-IIx/d; AltName: Full=Myosin heavy chain, skeletal muscle, adult 1 [Homo sapiens] >gi|119610411|gb|EAW90005.1| hCG1986604, isoform CRA_b
MSSDSEMAIFGEAAPFLRKSERERIEAQNKPFDAKTSVFVVDPKESFVKATVQSREGGKVTAKTEAGATVTVKDDQVFPM
NPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQEAPPHIFSISD
NAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGEKKKEEVTSGKMQGTLEDQIISANPLLEAFGNAKTVR
NDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNPYDYAFVSQGE
ITVPSIDDQEELMATDSAIEILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYLQNLNSADLLK
ALCYPRVKVGNEYVTKGQTVQQVYNAVGALAKAVYDKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEIFDFNSLEQLC
INFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTSFKNKLYEQHL
GKSNNFQKPKPAKGKPEAHFSLIHYAGTVDYNIAGWLDKNKDPLNETVVGLYQKSAMKTLALLFVGATGAEAEAGGGKKG
GKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICRKGFPSRILYA


##</code><code>##

Homo sapiens
MSSDSEMAIFGEAAPFLRKSERERIEAQNKPFDAKTSVFVVDPKESFVKATVQSREGGKVTAKTEAGATVTVKDDQVFPM
NPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQEAPPHIFSISD
NAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGEKKKEEVTSGKMQGTLEDQIISANPLLEAFGNAKTVR
NDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNPYDYAFVSQGE
ITVPSIDDQEELMATDSAIEILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYLQNLNSADLLK
ALCYPRVKVGNEYVTKGQTVQQVYNAVGALAKAVYDKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEIFDFNSLEQLC
INFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTSFKNKLYEQHL
GKSNNFQKPKPAKGKPEAHFSLIHYAGTVDYNIAGWLDKNKDPLNETVVGLYQKSAMKTLALLFVGATGAEAEAGGGKKG
GKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICRKGFPSRILYA