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csv_to_gene_db - generate the appropriate headers for srst2

CSV_TO_GENE_DB(1) User Commands CSV_TO_GENE_DB(1)

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.
June 2016 csv_to_gene_db 0.1.8