parsePrimer3Output: Parse Primer3 Output

In argschwind/TAPseq: Targeted scRNA-seq primer design for TAP-seq

Parse Primer3 Output

Description

Parse Primer3 output and add to input TsIO or TsIOList object. This function is usually not used by the user, as designPrimers handles Primer3 output parsing.

Usage

parsePrimer3Output(object, primer3_output)

Arguments

object	The TsIO or TsIOList object used to design primers. No errors or warnings if this is a different TsIO or TsIOList object!
primer3_output	Character vector containing raw Primer3 output.

Value

TsIO or TsIOList object with added Primer3 output

Examples

## Not run: 
# chromosome 11 truncated transcript sequences
data("chr11_truncated_txs_seq")

# create TsIOList object for the first two sequence templates
tapseq_io <- TAPseqInput(chr11_truncated_txs_seq[1:2], product_size_range = c(350, 500))

# create boulder IO records
io_record <- createIORecord(tapseq_io)

# design primers and store raw Primer3 output
primer3_core <- getOption("TAPseq.primer3_core")
primer3_output <- system2(command = primer3_core, input = io_record, stdout = TRUE)

# parse output and add it to input TsIO object(s)
tapseq_io <- parsePrimer3Output(tapseq_io, primer3_output)
tapseq_primers(tapseq_io)

## End(Not run)

argschwind/TAPseq documentation built on Feb. 9, 2024, 8:20 p.m.