RUN_MAPPERS(1)

💖 run_mappers — the vibe check 💖

okay bestie, so this is run_mappers, a User Commands girlie (section 1, iykyk) and she's literally here to run a read mapper and map your reads to reference genomes. no cap. 🧬✨

✨ NAME ✨

run_mappers — run a read mapper to map reads to reference genomes 🫶

🌸 SYNOPSIS 🌸

run_mappers NAMES READS -i REF -o OUT -m MAPPER

🦋 DESCRIPTION 🦋

So like, the whole point? Run a read mapper to map reads to reference genomes. That's it, that's the job. 💅

The names in the NAMES file will be inserted into the provided string patterns. Each pattern must contain exactly one "%s" placeholder — that's python string formatting, babe, not a suggestion. One. %s. Periodt. 🙈

👑 OPTIONS 👑

• NAMES — Filename of the names file. The plain text names file should contain one name per line. That name is used as the identifier in the whole algorithm. main character energy, fr fr. ⭐
• READS — File containing the reads to be mapped. your lil reads, off to get mapped 🍓
• -h, --help — show this help message and exit. iconic behaviour honestly 💅
• -m MAPPER, --mapper=MAPPER — Identifier of mapper defined in core/tools.py [default: none]. lowkey important that you actually set this one, bestie 😭
• -i REF, --index=REF — Pattern that points to the reference sequences/indices when used with a name. Placeholder for the name is "%s". [default: ./ref/%s.fasta] 🧬
• -o OUT, --output=OUT — Pattern that points to the output SAM file, when used with a name. Placeholder for the name is "%s". [default: ./SAM/%s.sam] ✨

heads up bestie: both -i and -o are patterns, not plain paths, and both need their "%s" or the name ain't going nowhere. and -m defaults to none, so like… do with that information what you will. 🙈

that's the whole page, you ate that 💖 go map some reads 🧚

mwah 💋 this was run_mappers SVNr18, brought to you way back in February 2014 — she's been serving since 2014 and she's still slaying 🎀