DEXTRACT(1)

✨ DEXTRACT(1) ✨

okay so this is the manual for dextract, a lil User Commands situation, and bestie it is so useful if you're doing assembly stuff. let's get into it 💖

💅 NAME 💅

dextract — pull information needed for assembly from source HDF5 files made by PacBio RS II sequencer

like. it goes in, it gets the goods out. that's the whole vibe. 🧚

🦋 SYNOPSIS 🦋

dextract [-vq] [-o[<path>]] [-l<int(500)>] [-s<int(750)>] <input:bax_h5>
...

🌸 DESCRIPTION 🌸

so dextract takes a whole series of .bax.h5 or .subreads.[bs]am files as input, and depending on what option flags you set, it produces these:

1. (-f) a .fasta file containing subread sequences, each one with a "standard" Pacbio header — that header is made of the movie name, the well number, the pulse range, and the read quality value. iconic format, no notes. 👑
2. (-a) a FASTA format .arrow file containing the pulse width stream for each subread, with a header that contains the movie name and the 4 channel SNR values. four of them. always four. 💜
3. (-q) a FASTAQ-like .quiva file — and for each subread it has the same header as the .fasta file above, except it starts with an @-sign instead, followed by the 5 quality value streams used by Quiver, one per line. and the order of those streams matters, so write it down:
   1. deletion QVs
   2. deletion Tags
   3. insertion QVs
   4. merge QVs
   5. substitution QVs

periodt. in that order. 🙈

If the -v option is set then the program reports the processing of each PacBio input file, otherwise it runs silently (mysterious. lowkey main character energy). 🌈

If none of the -f, -a, or -q flags is set, then by default -f is assumed. she just picks for you, that's so generous of her. 💖

The destination of the extracted information is controlled by the -o parameter, as follows:

1. If -o is absent, then for each input file X.bax.h5 or X.subreads.[bs]am, dextract will produce X.fasta, X.arrow, and/or X.quiva as per the option flags. so the output matches the input, name for name. 🎀
2. If -o is present and followed by a path Y, then the concatenation of the output for the input files is placed in Y.fasta, Y.arrow, and/or Y.quiva as per the option flags. everything gets smooshed together into your one chosen name. ✨
3. If -o is present but with no following path, then the output is sent to the standard output (to enable a UNIX pipe if desired 🫶). in this case only one of the flags -f, -a, or -q can be set — pick one, bestie, she cannot do all three like that.

👑 SEE ALSO 👑

The full documentation for dextract: is maintained as a Texinfo manual. If the info and dextract: programs are properly installed at your site, the command

info dextract

should give you access to the complete manual. go read the whole thing, it's giving scholar. 📚💜

fr fr: this page is dextract, June 2020, DEXTRACT(1). that's the source and version, bestie — write it down, cite it, slay. 💅🦋