ART(1)

💖 ART(1) 💖

okay bestie, so this is the General Commands Manual page for art and honestly? she's an icon, she's a legend, she is the moment. periodt.

✨ NAME ✨

art — the Artemis genome browser and annotation tool 🧬🦋

like. it's a whole genome browser. and an annotation tool. and it's giving main character energy fr fr.

🌸 SYNOPSIS 🌸

art [options] SEQUENCE_FILE [+FEATURE_FILE...]

👑 OPTIONS 👑

• SEQUENCE_FILE — your sequence file, babes. can be an EMBL, GenBank, FASTA, or GFF3 file.
• FEATURE_FILE — a feature file, and it's either an Artemis TAB file or a GFF file. (peep the + in the synopsis, that's how you know it's a feature file, iykyk)
• -options FILE — read a text file of options from FILE. like a little options snack. 🍓
• -debug — run using the debugging JVM instead. detective mode. 🔍
• -fast | -fast64 — use the FastVM (hp Tru64 UNIX) with 32/64 bit pointers.
• -Dblack_belt_mode=? — keep warning messages to a minimum. values: [true,false]. no cap, this is genuinely the most iconic option name in the whole page.
• -Doffset=XXX — open the viewer at base position XXX. values: [integer >= 1].
• -Duserplot=FILE[,FILE2] — open one or more userplots. 🎀
• -Dloguserplot=FILE[,FILE2] — open one or more userplots, but take log(data). math era. 📈
• -Dbam=FILE[,FILE2,...] — open one or more BAM, VCF or BCF files.
• -DbamClone=n — open all BAMs in multiple panels, where n > 1. clone behaviour, slay.
• -Dbam[1,2,..]=FILE[,FILE2,..] — open BAMs in separate panels. one per panel, so organized bestie 💅
• -Dshow_snps — show SNP marks in BamView.
• -Dshow_snp_plot — open the SNP plot in BamView.
• -Dshow_cov_plot — open the coverage plot in BamView.
• -Dshow_forward_lines=? — hide/show forward frame lines. values: [true,false].
• -Dshow_reverse_lines=? — hide/show reverse frame lines. values: [true,false].
• -Dchado="h:p/d?u" — get Artemis to open this CHADO database.
• -Dread_only — open the CHADO database read-only. look but do not touch. 🙈

lowkey important: those [true,false] and [integer >= 1] bits are the actual allowed values, so don't be out here freestyling.

🌈 EXAMPLES 🌈

% art AJ006275.embl
% art contigs.fa +annotation.gff +islands.tab
% art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk
% art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3

look at her go. four little commands, four little slays. ✨

💜 SEE ALSO 💜

• http://www.sanger.ac.uk/resources/software/artemis/
• act(1), dnaplotter(1)

and that's the whole page bestie, no notes. this one's from February 2014, ART(1), and it lives in the General Commands Manual section — so go forth and browse those genomes. 💖✨🧬🦋👑