since you have two loops you can or integrate when you grab $id or just before opening the filehandle:

But, looking more closer to your code, you have many wrong things:

my %id2seq = (); # this is the verbose form of my %id2seq;
my $id = '';     # this is the wrong place to declare this var! declar
+e it when you need it ie
                 # inside the while(<File>){ block
         # missing the mode: put always even if it defaults to '<'
open File,"human_hg19_circRNAs_putative_spliced_sequence.fa",or die $!
+;
         # better use lexical filehandle like in open my $fh, '<', $fi
+lepath or die
         # bareword is still accepted but by onvention is UPPERCASE so
+ no open File...

    while(<File>){
        chomp;
                 # here you are capturing something: if you want just 
+the part before | you
                 # have here the possibility to get it:  /^>([\w\d]+\|
+)/ as starting option?
        if($_ =~ /^>(.+)/){
                 # or here:
                 $id = $1;
                 # cutting $1 like in: $id = (split /\|/, $1)[0]
...
           # AHHH! this is error! are your use strict; use warnings ju
+st make-up?
           # it must be foreach my $id ..
           # (or really does not raise a warn for the scope you given 
+to $id ??? if so is even
           #  worst!!)
           # in short: pay attention to the scope of your variables
   foreach $id (keys %id2seq){
                 # here the last good possibility to cut $id:
                 # $id = (split /\|/, $id)[0];
        if (-f $id){                             # this is a lie..
            print $id." Already exists, about to override it","\n"
        }                 # .. because you are going to append, not to
+ overwrite
        open  my $out_fh, '>>', "$id.fa" or die $!; 
                     # here parens are unneeded and probably nasty
        print $out_fh (">".$id."\n",$id2seq{$id}, "\n");
[download]

L*

But the thing is, I want to be able to capture the full fasta sequence title (>hsa_circ_0000001|chr1:1080738-1080845-|None|None) along with the sequence and print that into a file and I want to capture a part of the sequence title and use it to name the file (hsa_circ_0000001) excluding '>'.

If I use your method surely I will not be able to print the full fasta sequence title followed by a newline and then the sequence in my newly created file, because $id will become (hsa_circ_0000001), whereas I need to be able to capture both (hsa_circ_0000001) and (>hsa_circ_0000001|chr1:1080738-1080845-|None|None) and apply them seamlessly as the new files are created in my loop.

Pete.

If so create a new variable for the filename, just before creating the file, as in

 

foreach $id (keys %id2seq){
                 # here the last good possibility to cut $id:
                 my $filename = (split /\|/, $id)[0];
                 ...
[download]

L*

There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.

Okay, I fixed up the items you suggested I should, and so my script is looking like this:

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


open my $fh, '<',"human_hg19_circRNAs_putative_spliced_sequence.fa",or
+ die $!;

my %id2seq;

    while(<$fh>){
        my $id = '';
        chomp;
        if($_ =~ /^>(.+)/){
            $id = $1;
        }else{
            $id2seq{$id} .= $_;
        }
    }

 

    foreach my $id (keys %id2seq){
        my $filename = (split /\|/, $id)[0];
        open  my $out_fh, '>>', "$filename" or die $!; 
        print $out_fh ">".$id."\n",$id2seq{$id}, "\n";
        close $out_fh;
    }


close $fh;
[download]

How do I integrate the value I've split and extracted into the naming of the file, because it's stating that it's uninitialised?

Although, I thought that it was clearly initialised/defined here:

  my $filename = (split /\|/, $id)[0];
        open  my $out_fh, '>>', "$filename" or die $!;
[download]

Or maybe I'm just misunderstanding the scope? Where do I place the $filename in the loop?

Pete.

The problem is earlier where $id is set for the > lines but then cleared on the subsequent sequence lines

while(<$fh>){
  my $id = '';
  chomp;
  if ($_ =~ /^>(.+)/){
    $id = $1;
  } else {
    $id2seq{$id} .= $_;
  }
}
[download]

Try

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

my $id;
my %id2seq;

my $infile = 'human_hg19_circRNAs_putative_spliced_sequence.fa';
open my $fh,'<',$infile 
     or die "Could not open $infile : $!";
while (<$fh>){
  if ( /^>(.+)/ ){
    $id = (split /\|/, $1)[0];
  }
  $id2seq{$id} .= $_;
}

foreach my $id (keys %id2seq){
  my $filename = $id.'.fa';
  print "Creating $filename\n";
  open my $out_fh,'>', $filename 
       or die "Could not open $filename : $!";
  print $out_fh $id2seq{$id};
  close $out_fh;
}

close $fh;
[download]

poj

Did you try printing the values of your variables as I suggested?



The way forward always starts with a minimal test.

Okay, so I tried to implement that as so:

    foreach $id (keys %id2seq){
        my $filename = (split /\|/, $id)[0];
        open  my $out_fh, '>>', "$filename.fa" or die $!; 
        print $out_fh (">".$id."\n",$id2seq{$id}, "\n");
        close $out_fh;
    }
[download]

But I got an error saying that $filename was uninitialized at the 3rd line down ---  open  my $out_fh, '>>', "$filename.fa" or die $!;

So I'm just trying to figure out where I should be declaring  $filename

Pete.

First, follow the advice given. Go through your script and correct *all* the items Discipulus pointed out. Second, when in doubt, print out the value of your variables.

use Data::Dumper;
...
foreach my $id (keys %id2seq) {
    warn "ID: $id";

    my @segments = split /\|/, $id;
    warn "Segments: " . Dumper \@segments;

    my $filename = $segments[0];

    ...
}
[download]

Once the code is working right, remove the debug statements.


The way forward always starts with a minimal test.

No, you got the error saying that $filename.fa is uninitialized.
So perl saw that as a variable name while you intended to only use $filename instead.
In order to delimit the variable name you can use this syntax: "${filename}.fa".
Good luck, hexcoder

Thank you for this advice,it's golden, I will try to implement all your points today.

Pete.