BUILD_BLAST_ATLAS(1)

💖 BUILD_BLAST_ATLAS 💖

okay bestie, welcome to build_blast_atlas(1), a lil user command that is lowkey a whole icon ✨

🌸 NAME 🌸

build_blast_atlas — visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences 🧬🦋

🎀 DESCRIPTION 🎀

✨ USAGE ✨

build_blast_atlas -i FILE [-p DIR] [Options]
build_blast_atlas -p DIR [Options]

💅 DESCRIPTION 💅

So the way this works, bestie: you run this command twice in its little life. First to create a blast atlas project directory, then again to generate the maps. It's giving "two-phase main character energy" 👑

Run it with the -i option plus a GenBank file and boom 💥 — you get a brand new project using that GenBank file as the reference genome. Or, if you'd rather start from nothing, use the -p option and you get a blank project, in which case you gotta drop a reference GenBank file into the reference_genomes directory yourself. After the project exists, put the genomes you wanna compare against the reference into the comparison_genomes directory. No cap. 🫶

[Optional] You can go tweak the *.conf files to configure how the maps get drawn, and add extra GFF files to the features and analysis directories. Customize away, gorgeous 💖

Then you draw the maps by running this command again, this time with -p pointing at the project directory. Iconic. 🔥

👑 REQUIRED ARGUMENTS 👑

• -i, --input FILE — Sequence file in GenBank format, with a .gbk extension. This one's only required when you're first creating a blast atlas project. The project directory gets named after this file, unless you also pass the -p option. 🌸
• -p, --project DIR — Kicks off map creation for the project. If no project exists yet, a blank project gets created instead. When you use it together with the -i option, this is where the project is created. Only required when creating the blast atlas maps. ✨

🌈 OPTIONAL ARGUMENTS 🌈

• -m, --memory STRING — Memory value for Java's -Xmx option (Default: 1500m). 💾
• -c, --custom STRING — Custom settings for map creation. 🎨
• -b, --max_blast_comparisons INTEGER — Maximum number of comparison genomes to display (Default: 100). 🙈
• -z, --map_size STRING — Size of custom maps to create. If you wanna quickly regenerate new map sizes, use this option together with the --start_at_xml option. Possible sizes include small/medium/large/x-large, or a combination separated by commas (e.g. small,large). The size(s) you provide here will override the size(s) in the configuration files. 📏
• -x, --start_at_xml — Jump to XML generation. Skips performing blast, which can speed up map generation if blast has already been done. This option is for creating new maps after you've made changes to the .conf files. Note that any changes in the .conf files related to blast will be ignored. Also, this option will be ignored if the --start_at_map option is also provided. ⚡
• -r, --start_at_map — Start at map generation. Skips performing blast and generating XML. Useful if manual changes to the XML files have been made, or if you're creating new map sizes (see --map_size). 🗺️
• -h, --help — Show this message. We love a helpful queen. 👑

💀 NOTE 💀

This script will likely not work if there are spaces in the path to the project directory, because the NCBI tool formatdb cannot handle such paths. So pls, no spaces in your paths, bestie 😭🙏

💜 AUTHOR 💜

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

and that's a wrap, my love 💖 this whole thing is build_blast_atlas version 20170919, dated August 2018 — slay, periodt ✨🎀🦋