Converts CSV containing primers (one per row) to a FASTA file. If the output is to be used in other multiplex wormhole functions, primer sequences must be in the format sequenceID.#.FWD & sequenceID.#.REV - e.g., MACA01.0.FWD and MACA01.0.REV signify the “0th” set of primers that amplify the “MACA01” template.
import multiplex_wormhole as mw
mw.CSVtoFASTA(IN_CSV, OUT_FA, ID_FIELD="PrimerID", SEQ_FIELD="Sequence", ENCODING=sys.getfilesystemencoding())
cd ~/multiplex_wormhole #navigate to where your mw scripts live
python3 CSVtoFASTA.py -i INCSV -o OUTFA [-p PRIMERIDFIELD] [-s SEQFIELD] [-e CSV_ENCODING]
IN_CSV (-i) : CSV containing primer sequences. Must have ID_FIELD and SEQ_FIELD.
OUT_FA (-o) : Filepath to output FASTA.
ID_FIELD (-p) : Column name for primer names. [Default: PrimerID]
SEQ_FIELD (-s) : Column name for primer sequences. [Default: Sequence]
ENCODING (-e) : Encoding of CSV file. [Default: system encoding]