---
name: "csv_to_gene_db"
section: "1"
platform: "linux"
package: "srst2"
version: "0.2.0-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/csv_to_gene_db"
---

# csv\_to\_gene\_db(1)

generate the appropriate headers for srst2

## 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.