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.