csv_to_gene_db - generate the appropriate headers for srst2

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

csv_to_gene_db 0.1.8                                June 2016                                  CSV_TO_GENE_DB(1)

       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)

       csv_to_gene_db - generate the appropriate headers for srst2

-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

csv_to_gene_db [options]