I have a sample subroutine that parses through two fasta-formatted files containing several genes/gene sequences and returns two sets of hashes: one with values as nucleotide sequences, and another with values as description information - both have gene names as keys.

Ultimately, I want to print the hash information into two separate files in fasta format (i.e. gene name and description in header, then sequence underneath, for each gene). However, I don't know how to print the information to the files in the correct format - any suggestions how to do this?

Here's my code so far

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

my ($file1, $file2) = @ARGV;    
my $out1 = 'output1.fasta';
my $out2 = 'output2.fasta';

open (FILE1, "<$file1") or die "Cannot open input file: $file1 !\n";
open (FILE2, "<$file2") or die "Cannot open input file: $file2 !\n";
open (my $output1, ">$out1") or die "Cannot open output file: $out1 !\
+n";
open (my $output2, ">$out2") or die "Cannot open output file: $out2 !\
+n";

my @file1=<FILE1>; 
my @file2=<FILE2>;

my %File1=(); 
my %File1_D=();
my %File2=();
my %File2_D=();

Parse2Files (\@file1, \@file2, \%File1, \%File2, \%File1_D, \%File2_D)
+;

my @temp1a = keys %File1;     ## gene name
my @temp1b = values %File1_D; ## description
my @temp1c = values %File1;   ## gene seq

print $output1 "@temp1a, @temp1b, @temp1c\n";

my @temp2a = keys %File2;      ## gene name
my @temp2b = values %File2_D;  ## description
my @temp2b = values %File2;    ## gene seq

print $output2 "@temp2a, @temp2b, @temp2c\n";

sub Parse2Files {
    my ($arrayref1, $arrayref2, $hashref1, $hashref2) = @_;

    my @file1=@{$arrayref1};
    my @file2=@{$arrayref2};

    my $f1dscp='';                ## File 1 - fasta description
    my $f1name='';                ## File 1 - fasta gene name
    my $f2dscp='';                ## File 2 - fasta description
    my $f2name='';                ## File 2 - fasta gene name
    
    for (my $i=0; $i<=$#file1; $i++) {  
        chomp($file1[$i]);                                    
    
        if ($file1[$i] =~ m/^>(\S+)\s(.+)/) {
            $f1name = $1;    
            $f1dscp = $2;
            $File1_D{$f1name} = $f1dscp;
        }
        else{
            $File1{$f1name} .= $file1[$i];   
        }
    }

    for (my $i=0; $i<=$#file2; $i++) {   
        chomp($file2[$i]);                                    
    
        if ($file2[$i] =~ m/^>(\S+)\s(.+)/){
            $f2name = $1;
            $f2dscp = $2;
            $File2_D{$f2name} = $f2dscp;
        }
        else{
            $File2{$f2name} .= $file2[$i];  
        }
    }
    return (%File1,%File2, %File1_D, %File2_D);
}
[download]

Yes, the code is basically taking two fasta files and putting them back into another fasta-formatted file - I'm just toying with this to practice making output filed.

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