Tuesday, August 12, 2014

Merge two kmer count hashes into one

 use warnings;  
 # Input parameters  
 open FASTA1, $ARGV[0] or die $!;  
 open FASTA2, $ARGV[1] or die $!;  
 my %seqs = ();  
 while($line = <FASTA1>){  
 chomp $line;  
 my @jelly=split(/\s+/,$line);  
 close FASTA1;  
 while($line = <FASTA2>){  
 chomp $line;  
 my @jelly=split(/\s+/,$line);  
 if(exists $seqs{$jelly[0]}){$seqs{$jelly[0]}=$seqs{$jelly[0]}+$jelly[1];}  
 close FASTA2;  
 foreach $iso (sort keys %seqs) {  
 print "$iso\t$seqs{$iso}\n";  

Will take two lists of kmer counts and merge them into one. A kmer count list consists of two columns. The first column being the kmer itself and the second being its count.

This might be useful in merging the output of a program like jellyfish after running it on each chromosome separately. While jellyfish has a merge function, it requires the hashes to be of equal size.

May be this can be re-written as a perl one liner...

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