CREATE_MATRIX(1)

💖 CREATE_MATRIX(1) 💖

okay bestie, gather round, because we're diving into create_matrix from the User Commands manual, and honestly? it's giving genome-science main character energy. ✨

🌸 NAME 🌸

create_matrix — calculate the genome abundance similarity matrix 🧬💅

🦋 SYNOPSIS 🦋

create_matrix [options] NAMES

✨ DESCRIPTION ✨

So like, the whole point of this icon is: calculate the similarity matrix. That's the assignment, and it ate. 💅

But the way it gets there is a three-step glow-up, and you need to know all three, fr fr:

1. First, a set of reads is simulated for every reference genome, using a read simulator from core/tools.py — you pick which one with -s. 🎀
2. Second, the simulated reads of each species get mapped against all reference genomes, using the mapper you specified with -m. 🌈
3. Third, the resulting SAM-files get analyzed to calculate the similarity matrix.

And where does that gorgeous matrix live? It gets stored as a numpy file — that's what -o is for. 🫶

👑 OPTIONS 👑

• NAMES — the filename of the names file, bestie. It's a plain text file and it should contain one name per line. That name is used as the identifier in the whole algorithm, so it's lowkey important. 🏷️
• -h, --help — show this help message and exit. the classic. the legend. 🙈
• -s SIMULATOR, --simulator=SIMULATOR — the identifier of the read simulator, as defined in core/tools.py. [default: none] ⭐
• -r REF, --reference=REF — reference sequence file pattern for the read simulator. the placeholder for the name is "%s". [default: ./ref/%s.fasta] 🍓
• -m MAPPER, --mapper=MAPPER — the identifier of the mapper, as defined in core/tools.py. [default: none] 🔥
• -i INDEX, --index=INDEX — reference index files for the read mapper. placeholder for the name is "%s". [default: ./ref/%s.fasta] 🧚
• -t TEMP, --temp=TEMP — directory to store temporary simulated datasets and SAM files. [default: ./temp] 🌸
• -o OUT, --output=OUT — output similarity matrix file. [default: ./similarity_matrix.npy] 💜

🫶 friendly reminder: those "%s" placeholders in -r and -i are literal — keep them exactly as they are, no cap. and yeah, -s and -m both default to none, so you're gonna wanna set those unless you enjoy chaos. 😭

and that's the whole page, bestie — this was create_matrix SVNr18, dated February 2014. iconic behavior, honestly. now go build that matrix. 💖✨🎀