Hello,

I'm trying to create subroutines for the functions in my script. My attempts so far don't produce the files of a specific length, although the second subroutine named, 'HashSequences' seems to work at least as far as for requesting minimum length and maximum length from the user, which of course is far from the objective.

I know it will be important to learn how to use subroutines because I have other ideas of functions I would like to implement into this script to eventually have a script that manipulates large files containing fasta sequences in many ways.

Here is my code:

##Invoking subroutines

HashSequences();
SpecifySeqLengths(my $id, my %seq);
## I got errors when I didn't declare these, yet somehow I think this 
+is wrong

## Open file. Hash sequences. Make the sequence IDs the keys to their
## respective (hashed) sequences.


sub HashSequences{

open F, "human_hg19_circRNAs_putative_spliced_sequence.fa", or die $!;

my %seq = ();
my $id = '';

while (<F>){
    chomp;
    if ($_ =~ /^>(.+)/){
        $id = $1;
    }else{
        $seq{$id} .= $_;
    }
}
close F;
return (%seq, $id);
}

## Request sequence length desired. Sieve sequences of given length 
## into arrays. Create file containing desired sequences.

sub SpecifySeqLengths{

print "Enter Max sequence length: \n";
my $maxlength = <STDIN>;
chomp $maxlength;

print "Enter Min sequence length: \n";
my $minlength = <STDIN>;
chomp $minlength;

my @seqarray;

foreach $id (keys %seq){
    if ((length$seq{$id} <= $maxlength) && (length$seq{$id} >= $minlen
+gth)){
        push @seqarray, $id;
    }
}

for $id (@seqarray){
    if (-f $id){print $id, " already exists. It is about to be overwri
+tten"};
    open new_F, '>>', "SeqLength_$minlength-$maxlength", or die$!;
    print new_F ($id."\n".$seq{$id}."\n");
    close new_F;
}

}

[download]

Any help is well appreciated

Thank you.

In reply to I'm trying to consolidate my functions into subroutines by Peter Keystrokes

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