How to convert genoma.fa to chr*.fa

[krafiq]

Dear dpryan,

I'm trying to use the hotspot software and I'm trying to run their enumerateUniquelyMappableSpace script on my custom genome file. However, we don't have chromosome information for my genome. The genome.fa file only has >scaffolds. Is there a way to run hotspot without separating the genome fasta file into chromosomes/obtaining chr*.fa for every chromosome?

[dpryan]

Do you mean to say that there are no ">chr..." lines in the Genome.fa file, only ">scaffold..." or something like that? If that's the case then there's no way to do it without assembling the scaffolds into chromosomes (which would take more sequencing and likely some wet-bench experiments).

If you mean to say that you have a mixture of ">chr..." and ">scaffold..." entries, then you can just modify the perl script above (just add a variable to store the context that you're in and only write output if you're in a ">chr..." context).

[krafiq]

Dear SNPsaurus,

Thanks for your response! Howevr, my genome.fa file contains scaffold files and not chr files. So if I use your code above, it would create one file per scaffold. How do I get to one chr*.fa file for each chromosome from here?

[SNPsaurus]

Hi krafiq,

Here is some Perl to do that. You just need to save it (as split.pl) to the folder you have your fasta file, then in the command line, write "perl split.pl genome.fa" where genome.fa is the name of your file. It will save a file for whatever is used as the header (I'm assuming it looks like ">chr1".

#!/usr/bin/perl

$f = $ARGV[0]; #get the file name

 open (INFILE, "<$f")
	or die "Can't open: $f $!";
		
while (<INFILE>) {
	$line = $_;
	chomp $line;
	if ($line =~ /\>/) { #if has fasta >
		close OUTFILE;
		$new_file = substr($line,1);
		$new_file .= ".fa";
		open (OUTFILE, ">$new_file")
			or die "Can't open: $new_file $!";
	}
	print OUTFILE "$line\n";
}
close OUTFILE;

[krafiq]

I am working with a genome file which is not on the USC genome browser. I have my own Genome.fa file and I want to separate the genome fasta file into chromosomes, so that there is one chr*.fa file for each chromosome.

Could someone please guide me as to how? I am just beginning to use Linux!

Thanks so much!