ACT(1)

✨ ACT ✨ (General Commands Manual, bestie, let's gooo) 💖

🌸 NAME 🌸

okay so act is the Artemis comparison tool for genome sequences 🧬 and it is literally so iconic. it's basically the app that lets you compare genome stuff side by side 💅

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🦋 SYNOPSIS 🦋

act [options] SEQUENCE_1 COMPARISON_1_2 SEQUENCE_2 ...

the vibe: you toss in your sequences and comparisons and act does the rest ✨

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🎀 OPTIONS 🎀

okay so there are three kinds of files you can hand it, bestie 🫶

• SEQUENCE — an EMBL, GenBank, FASTA, or GFF3 file 🧬
• FEATURE — an Artemis TAB file, or GFF file 🍓
• COMPARISON — a BLAST comparison file in tabular format 💜

and now the flags (it's giving options overload but make it cute) 🌈

• -options FILE — read a text file of options from FILE 📝
• -chado — connect to a Chado database, using the PGHOST, PGPORT, PGDATABASE, and PGUSER environment variables 🌷

the -D flags are where it gets spicy 🌶️

• -Dblack_belt_mode=? — keep warning messages to a minimum. the ? is true or false 🥋
• -DuserplotX=FILE[,FILE2] — for sequence X, open one or more userplots 📈
• -DloguserplotX=FILE[,FILE2] — for sequence X, open one or more userplots, and take log(data) 🪵
• -DbamX=FILE[,FILE2,...] — for sequence X, open one or more BAM, CRAM, VCF, or BCF files 🧬
• -Dchado="h:p/d?u" — tell ACT to open this CHADO database 🗂️
• -Dread_only — open the CHADO database read-only 🔒

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🧚 EXAMPLES 🧚

no cap, these are the ones you'll actually use 💅

% act
% act af063097.embl af063097_v_b132222.crunch b132222.embl
% act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf
% act -Duserplot2=/pathToFile/userPlot

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👑 SEE ALSO 👑

okay the big one to read is the Artemis ACT page 🌈

https://sanger-pathogens.github.io/Artemis/ACT/

and then you'll want these two as well 💖

• art(1)
• dnaplotter(1)

periodt, go be a genome legend 🫶✨ (September 2020 vibes, ACT(1) forever 💜)