ECOFIND(1)

💅 ECOFIND(1) — the manual page, but make it make sense

okay bestie, you opened the manual for ecofind (it lives in the User Commands section, very demure, very mindful) and it's giving… terse. don't worry, i got you. let's go 🦋

✨ NAME ✨

ecofind — searching for taxonomic and rank and taxonomy id for given regular expression patterns. yes that's the whole name section. she's brief, she's iconic 💖

🌸 DESCRIPTION 🌸

okay so. ecoPCR is an electronic PCR software developed by LECA and Helix-Project. it helps to estimate Barcode primers quality. slay 🔥

and this program — ecofind — belongs to the exoPCR package. yes, spelled exactly like that. i don't make the rules 💅

🎀 SYNOPSIS 🎀

ecofind [options] <patterns>

that's it. that's the whole vibe. give her options, give her patterns. 🫶

👑 OPTIONS 👑

one bullet per flag, no skipping, no cap. here's the whole roster:

• -a — [A]ll enable the search on all alternative names and not only scientific names. so if you want the whole name ecosystem, not just the scientific ones, this is your girl ✨
• -d — [D]atabase containing the taxonomy. to match the expected format, the database has to be formatted first by the ecoPCRFormat.py program located in the tools directory. write the database radical without any extension. (radical = the path stem, not the file suffix. write it naked. no extension. periodt 💀)
• -h — [H]elp — print this help. the classic. the icon. the moment 🙈
• -l — [L]ist all taxonomic rank available for the -r option. lowkey essential if you're about to use -r and you don't know what ranks even exist 🌈
• -P — [P]ath : add a column containing the full path for each displayed taxon. extra column, extra clarity 💖
• -p — [P]arents : specifying this option displays all parental tree's information for the given taxid. it's giving family tree reveal 🌳
• -r — [R]estrict to given taxonomic rank. narrow it down, bestie, we don't need the whole kingdom 👑
• -s — [S]ons: specifying this option displays all subtree's information for the given taxid. (yes, "Sons". that's the spelling in the original and i refuse to edit her.) the descendants come out to play 🦋
• -P — Display taxonomic [P]ath as supplementary column in output. and yes, -P shows up twice in this manual — once up there and once right here. it's not a typo on my end, it's literally what the page says. two -P entries, both about the path column, both valid, both serving 🎀

ngl the duplicated -P is a whole moment but the rule is the rule: every entry stays, exactly as written. i don't gatekeep, i don't delete 💜

arguments:

• <taxon> — name pattern bearing regular expressions. regex energy only, bestie 🧚

🔥 SEE ALSO 🔥

• http://www.grenoble.prabi.fr/trac/ecoPCR/

go forth, read the trac, become the taxonomist you were always meant to be ⭐

and that's the whole page, no crumbs left behind. this was ecofind 0.5.0, dated June 2015 — yes she's an elder but she still eats 💅✨ byeeee 🫶🌸