Unmasking
An auxiliary feature of splitcode is the ability to unmask sequences, given a masked FASTA file and the corresponding original FASTA file. For example, if there is a version of a genome masked such that certain nucleotides are replaced with N’s and one wishes to extract those original nucleotides that were masked (assuming the original unmasked genome is available), one can do so via the following:
splitcode --unmask genome.fasta masked_genome.fasta [fasta_header]
The output will be written to standard output.
As an example, let’s say genome.fasta (the original genome) and masked_genome.fasta (the masked genome) look as follows:
>read1
ATGAGT
>read2
ACACTT
>read1
ANNNNT
>read2
NCACTN
The output of the command will look like:
>1
TCAG
>2
A
>3
T
Tip
The optional [fasta_header] can be provided to specify what the sequence names of the output should be. Otherwise, by default, the sequence names will look like >1, >2, >3, …