BUILD_BLAST_ATLAS_ALL_VS_ALL(1)

👑 BUILD_BLAST_ATLAS_ALL_VS_ALL — the section 1 manual, bestie edition 💅

okay so welcome to the User Commands section of the manual, babes. this one's called build_blast_atlas_all_vs_all, it lives in manual section 1, and it is lowkey iconic for one specific thing: staring at bacterial, plasmid, chloroplast, or mitochondrial sequences until they make sense. 🦋

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✨ NAME ✨

build_blast_atlas_all_vs_all — visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences 🌸

like, it's giving "put all your little genomes on the same moodboard". 🎀

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🫶 DESCRIPTION 🫶

💖 USAGE:

build_blast_atlas_all_vs_all -p DIR [Options]

💜 DESCRIPTION:

okay so bestie, this script automatically generates several CCT projects, and then it combines all of those results into a single montage map. the montage is made of a separate map for each sequence of interest — which means every sequence in a group of sequences gets to be visualized as the reference sequence. main character energy for literally every genome, no cap. 👑

the way this command works is: you run it once to create a blast atlas all vs all project directory, and then you run it again to generate the montage. after the project has been created, you place the genomes you want to compare in the comparison_genomes directory. that's the whole vibe. ✨

[Optional] you can make changes to the project_settings_multi.conf file to configure how the maps will be drawn. you can also add additional GFF files to the features and analysis directories. go off, honestly. 🧚

then you draw the maps by running this command again with the -p option pointing at the project directory. periodt. 💅

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🌟 REQUIRED ARGUMENTS: 🌟

• -p, --project DIR — if no project exists yet, this creates a new project directory. otherwise, it initiates map creation for the project. it's the required one, bestie, you cannot skip it. 🙈

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🌈 OPTIONAL ARGUMENTS: 🌈

• -m, --memory STRING — the memory value for Java's -Xmx option. (Default: 1500m). feed the JVM, it's hungry. 🍓
• -c, --custom STRING — custom settings for map creation. your map, your rules. ✨
• -b, --max_blast_comparisons INTEGER — the maximum number of comparison genomes to display. (Default: 100). don't be greedy, okay? 😌
• -z, --map_size STRING — size of the custom maps to create. if you want to 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). whatever size(s) you provide will override the size(s) in the configuration files. slay. 💅
• -x, --start_at_xml — jump straight to XML generation. this skips performing blast, which can speed up map generation if blast has already been done. it's the move for creating new maps after you've made changes to the .conf files, or if you're creating new map sizes (see --map_size). ⚠️ 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 or --start_at_montage option is also provided. iykyk. 🔥
• -r, --start_at_map — start at map generation. this skips performing blast and generating XML. super useful if you've made manual changes to the XML files. this option will be ignored if the --start_at_montage option is also provided. 🙈
• -g, --start_at_montage — start at montage generation. this skips creating the individual maps. useful if you're changing how many columns the montage should have. montage-only era. 🎀
• -y, --columns INTEGER — the number of columns to use in the montage image. (Default: 4). if the maps have already been drawn once, it's best to use this option together with the --start_at_montage option. grid layout, but make it fashion. 🌸
• -h, --help — show this message. the classic. 🫶

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💀 NOTES: 💀

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 like… no spaces, bestie. i'm serious. 💀

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🌸 AUTHOR 🌸

this manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. king behavior, honestly. 👑

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okay that's the whole page!! this was build_blast_atlas_all_vs_all version 2..., dated August 2018, filed under BUILD_BLAST_ATLAS_ALL_VS_ALL(1) in the User Commands section. mwah, take care of your genomes, bye bestie!! 💖✨🎀🦋