MASON_MATERIALIZER(1)

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version 2.5.2 · 2 versions
, in ubuntu stonking

💖 MASON_MATERIALIZER(1) — the mason_materializer page, bestie edition 💖

okay so. this is the manual for mason_materializer and honestly? it's giving ✨VCF Materialization✨. buckle up, we're doing this together 🫶

✨ SYNOPSIS ✨

mason_materializer [OPTIONS] -ir IN.fa -iv IN.vcf -o OUT.fa

🌸 DESCRIPTION 🌸

You take the variants chillin' in IN.vcf, you apply them to IN.fa, and you write the results out to out.fa. That's the whole vibe. Slay 💅

🎀 OPTIONS 🎀

  • -h, --help — shows you the help message. iconic behaviour, tbh.
  • --version — tells you the version info. she's got receipts 💖
  • -q, --quiet — low verbosity. she's being lowkey 🤫
  • -v, --verbose — higher verbosity. she's talking more.
  • -vv, --very-verbose — highest verbosity. she will NOT stop talking 🔥
  • --seed UINT64 — seed for random number generation. Default: 0.
  • --meth-seed UINT64 — seed for methylation simulation random number generation. Default: 0.
  • -o, --out OUTPUT_FILE — the output of materialized contigs. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression. so many options bestie, pick your fighter 🌈
  • --out-breakpoints OUTPUT_FILE — a TSV file to write breakpoints in variants to. Valid filetypes are: .txt and .tsv.
  • --haplotype-name-sep STRING — the string that separates contig name from haplotype number. Default: /.
  • --meth-fasta-in INPUT_FILE — a FASTA file with the methylation levels of the input file. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
  • --meth-fasta-out OUTPUT_FILE — a FASTA file with the methylation levels of the output file. Valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

💜 Apply VCF Variants to Reference 💜

  • -ir, --input-reference INPUT_FILE — path to the FASTA file you're reading the reference from. ⚠️ heads up bestie: many contigs in a reference might be a problem because of all the file handles that need to be opened. Check the hard limit of file handles with ulimit -Hn and bump the soft limit up to the hard limit with ulimit -Sn <number> if you gotta. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
  • -iv, --input-vcf INPUT_FILE — path to the VCF file with the variants you wanna apply. Valid filetype is: .vcf[.*], where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.

🦋 Methylation Level Simulation 🦋

  • --methylation-levels — enable methylation level simulation. turn it ON 💅
  • --meth-cg-mu DOUBLE — median of the beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.6.
  • --meth-cg-sigma DOUBLE — standard deviation of the beta distribution for methylation level of CpG loci. In range [0..1]. Default: 0.03.
  • --meth-chg-mu DOUBLE — median of the beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.08.
  • --meth-chg-sigma DOUBLE — standard deviation of the beta distribution for methylation level of CHG loci. In range [0..1]. Default: 0.008.
  • --meth-chh-mu DOUBLE — median of the beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.05.
  • --meth-chh-sigma DOUBLE — standard deviation of the beta distribution for methylation level of CHH loci. In range [0..1]. Default: 0.005.

⭐ VCF VARIANT NOTES ⭐

okay so real talk, here's the tea ☕

If the option --input-vcf/-iv is given then the given VCF file is read and the variants are applied to the input reference file. If it is not given then the input reference file is taken verbatimly for simulating reads.

There are some restrictions on the VCF file, and the application of the variants to the reference will fail if the VCF file is non-conforming 😭 (no cap, it will not be okay about it). Good news though: VCF files from the mason_variator program are guaranteed to be read. we love a compatible queen 👑

Only the haplotypes of the first individual will be generated. so if you had hopes for the others... nope, she's not doing that today 🫶

💀 main character reminder: the vibe is immaculate but the rules are the rules — non-conforming VCF = it fails, periodt.

and that's the whole page, bestie!! this was mason_materializer 2.0.13 [tarball], dated in the MASON_MATERIALIZER(1) era, and honestly? we ate. go materialize some variants, you got this 💖✨🎀🦋🌸💅

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