NAME

       csv_to_gene_db - generate the appropriate headers for srst2

SYNOPSIS

       csv_to_gene_db [options]

DESCRIPTION

       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)

       -c HEADERS_COL, --headers_col=HEADERS_COL
              column number that contains the sequence names that match the fasta file headers

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.