Overview
Generates a set of control sequences from a set of reference sequences that are passed in. The goal is to maintain the statistical parameters (i.e. nucleotide composition) of the reference sequences without recapitulating the sites of interest.
How it works
All of the reference seqeunces are concatenated into one string. Random units are resampled from the conglomerate stirng and concatenated to make a control sequence.
Usage
cs_gen()
The parameters can be passed directly into the function. It will return the set of control sequences:
| Parameter | Default | Desrciption |
|---|---|---|
fasta_files |
input.fasta | path to a FASTA file containing the set of reference sequences to pull from to make the control sequences. |
output_file |
data/cs_gen.fasta | path to the output file where generated control set will be written. |
output_descrip |
Control sequence | THe description that is attached to each of the generated sequences in the output FASTA |
mark_param |
5 | Markovnikov parameter, the length of the resampling unit. (i.e. 5 -> fragments of length 5 will be selected) |
length |
1000 | The length of each individual control sequence |
num_seq |
100 | The number of control sequences to be returned. |
cs_genj()
An input JSON file is parsed for the parameters. JSON file layout:
{
"fasta_files" : ["data/input.fasta", "data/input2.fasta"],
"output_file" : "cs_gen.fasta",
"output_descrip" : "Control Sequence",
"mark_param": 5,
"length" : 10,
"num_seq" : 10
}