CSV_TO_GENE_DB(1)

🧬 csv_to_gene_db — the SRST2 header glow-up machine 💅

okay bestie, so this is csv_to_gene_db, a little User Commands moment from the SRST2-verse, and she's here to generate the appropriate headers for srst2. that's the whole job. no cap. 🎀

✨ SYNOPSIS ✨

csv_to_gene_db [options]

like. that's it. options only, babe. 🦋

🌸 DESCRIPTION 🌸

first things first: this tool is part of the SRST2 suite. she's not a lone wolf, she's in a friend group. 🫶

so what does she do. okay so imagine you have a csv table detailing clustering etc. (yes, the literal "etc.", we're keeping it) and you have sequences for your gene DB. this tool takes those and writes them out as fasta, in the csv file format that's expected, which looks like this:

seqID,clusterid,gene,allele,(DNAseq),other....

the headers in the output will be srst2 compatible, meaning they come out looking like:

[clusterID]__[gene]__[allele]__[seqID] [other stuff]

and the sequence itself? you've got two vibes to pick from, bestie:

1. read it from a specified column in the table, or
2. read it from a fasta file — and if you do that, you must specify which column in the table contains the sequence names that match the fasta file headers.

pick your fighter. 💜

🎀 OPTIONS 🎀

• -h, --help — show this help message and exit. the classic. the icon. she's always there for you. 🙈
• -t TABLE_FILE, --table=TABLE_FILE — table to read (csv). this is your input csv, your main character data source. 📄
• -o OUTPUT_FILE, --out=OUTPUT_FILE — output file (fasta). where the glow-up gets written. 💾
• -s SEQ_COL, --seq_col=SEQ_COL — column number containing sequences. tell her which column has the actual sequence, and she'll grab it from there. 🔢
• -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). so if your seqs live in a fasta instead of a column, this is your girl — but you have to tell her which column holds the names that match up with the fasta headers. no column, no match, no slay. ⚠️
• -c HEADERS_COL, --headers_col=HEADERS_COL — column number that contains the sequence names that match the fasta file headers. this is the matching key for the --fasta route, and yeah, it's mandatory when you go that way. 🔑✨

👑 AUTHOR 👑

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

and that's the whole page, bestie!! this was csv_to_gene_db 0.1.8, dated June 2016, and she still eats. periodt. 💖✨🦋🌸💅