mclblastline(1)

✨ mclblastline(1) ✨

okay bestie, so this is the manual page for mclblastline, and it lives in section 1 of the USER COMMANDS manual. pull up a chair, grab a strawberry 🍓, we're doing pipeline lore today.

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💖 NAME 💖

mclblastline — a whole pipeline for clustering, starting straight from BLAST files. it's giving "one command, so much happening" 👑

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🌸 SYNOPSIS 🌸

mclblastline file-name

mclblastline [deblast options] [pipeline options] file-name

✨ NOTE (the first one) ✨ so mcl lowkey leveled up and can now go straight from label input, the kind mcxdeblast produces. that unlocks a super lightweight way to make clusterings straight out of BLAST files. you might genuinely want to use this mechanism — it's documented over in the mcl manual. iykyk 💅

✨ NOTE (the second one, and it's a glow-up) ✨ mclblastline used to need the zoem macro processor hanging around (with default parameters, anyway) to produce its detailed output. not anymore bestie. by default mclblastline now makes a line-based tab-separated dump file. zoem only gets invoked when you pass the --fmt-fancy option. and in that case, yeah, zoem obviously has to be installed. no zoem, no fancy. 🙈

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🦋 DESCRIPTION 🦋

mclblastline is a wrapper around mclpipeline, okay? it hands over the --parser=app and --parser-tag=str options, setting them to mcxdeblast and blast respectively. translation: it's telling mclpipeline to use mcxdeblast as the parse script in its pipeline. 💫

the significance of that blast tag? any mcxdeblast option can be passed through mclblastline and mclpipeline by inserting the tag into the option. for example, mcxdeblast accepts the --score=x option. when you're using mclblastline, you write it as --blast-score=x. 🎀

there are two exceptions to this rule, and they are the --xi-dat=str and --xo-dat=str options. refer to the mclpipeline manual for more info on those. 👀

also, and this is the fun part, all mclpipeline options are acceptable to mcxdeblast as well. the --whatif option is amazing for getting a feel for the pipeline — it's the vibe check of options. the --mcl-I=f inflation option and --mcl-scheme=i scheme index options are your basic means for manipulating cluster granularity and allocating resources respectively. read the mcl manual entries for a description of the corresponding -I and -scheme mcl options. 🔥

the best advice honestly? glance over the mcxdeblast and mclpipeline options just to get a feeling for which ones might come in handy for you. then start experimenting. use --whatif, because it will tell you what would happen without actually doing it. main character energy fr fr. ✨

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💅 OPTIONS 💅

• All mcxdeblast and mclpipeline options. — that's it, that's the list. but heads up: mcxdeblast options must be passed using the mechanism described above (the --blast- tag trick). 🫶

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🌈 EXAMPLES 🌈

mclblastline --blast-score=b
   --blast-sort=a --blast-bcut=5 --mcl-I=2.5 myblastfile

this one will use bit scores, sort cluster indices so that the corresponding labels are ordered alphabetically, ignore bit scores not exceeding 5, and use an inflation value of 2.5. 💖

in this case, the output clustering lands in the file named myblastfile.I25s2 (where I25 identifies the inflation value and s2 identifies the resource scheme), and the formatted output lands in the file myblastfile.I25s2.fmt. two files, one command, slay. 🎀

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mclblastline --prepare-mcl myblastfile
mclblastline --start-mcl --mcl-I=1.2 myblastfile
mclblastline --start-mcl --mcl-I=1.6 myblastfile
mclblastline --start-mcl --mcl-I=2.0 myblastfile
mclblastline --start-mcl --mcl-I=2.4 myblastfile
mclblastline --start-mcl --mcl-I=2.8 myblastfile
etc ..

the first run prepares an input matrix to be read by mcl. in this case its file will be named myblastfile.sym. the subsequent runs use that matrix. ⭐

⚠️ CAVEAT bestie, listen up ⚠️ there are some options you need to repeat when you do a resumed run like this. they're clearly marked in the mclpipeline manual — namely those options that affect names of (intermediate) files. most importantly, this concerns the mclpipeline options that have prefix --xo or --xi. for example:

mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=1.2 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=1.6 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=2.0 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=2.4 myblastfile
mclblastline --start-mcl --xo-dat=b --mcl-I=2.8 myblastfile
etc ..

in this case the matrix file will be named myblastfile.b.sym, and the --xo-dat options must be repeated in all runs so that the pipeline reconstructs the correct file name(s). do not skip them, i'm begging. 😭

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👑 AUTHOR 👑

Stijn van Dongen — the icon who wrote this.

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🧚 SEE ALSO 🧚

mcxdeblast, mclpipeline, mcxassemble.

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and that's the whole page, bestie! this one's from mclblastline version 14-137, dated 16 May 2014, and yes it's still out here being mclblastline(1) in section 1. go cluster something. periodt. 💜🦋