csv_to_gene_db1
Generate the appropriate headers for srst2
Usage
csv_to_gene_db [options]
Overview
This tool is part of the SRST2 suite.
take csv table detailing clustering etc and sequences for gene DB, write as fasta expected csv file format:
-
seqID,clusterid,gene,allele,(DNAseq),other....
headers in output will be srst2 compatible, ie [clusterID]__[gene]__[allele]__[seqID] [other stuff] sequence can be read from a specified column or from a fasta file (specify which column contains fasta header to match in seqs file)
Options
-
-h, --help -
show this help message and exit
-
-t TABLE_FILE, --table=TABLE_FILE -
table to read (csv)
-
-o OUTPUT_FILE, --out=OUTPUT_FILE -
output file (fasta)
-
-s SEQ_COL, --seq_col=SEQ_COL -
column number containing sequences
-
-f FASTA_FILE, --fasta=FASTA_FILE -
fasta file to read sequences from (must specify which column in the table contains the sequence names that match the fasta file headers)
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-c HEADERS_COL, --headers_col=HEADERS_COL -
column number that contains the sequence names that match the fasta file headers