CGVIEW_COMPARISON_TOOL(1)

💖 CGVIEW_COMPARISON_TOOL(1) 💖

okay bestie, welcome to cgview_comparison_tool — a lil command-line icon that does the whole visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences thing. it lives in section 1 of the manual (user commands, obvs), and it is genuinely so good at what it does. let's get into it 🧚

✨ NAME ✨

cgview_comparison_tool — for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences. that's the whole vibe. periodt.

🌸 DESCRIPTION 🌸

🫶 USAGE:

cgview_comparison_tool -p DIR [options]

🦋 DESCRIPTION:

okay so here's the flow, and it's a two-step main character arc:

1. Run this command once to generate a project directory. ✨
2. After the project is created, drop a reference genome in the reference_genome directory, and any genomes you wanna compare against the reference go in the comparison_genomes directory. no cap.
3. (optional) Make changes to the project_settings.conf file to configure how the maps will be drawn. You can also add additional GFF files to the features and analyis directories.
4. Draw maps by running this command again with the -p option pointing to the project directory. slay. 💅

💅 REQUIRED ARGUMENTS:

• -p, --project DIR — the one thing you literally cannot skip. If no project exists yet, a blank project directory will be created. If the project does already exist, maps will be created. lowkey the whole personality of the tool tbh.

🎀 OPTIONAL ARGUMENTS:

• -s, --settings FILE — the settings file. If you don't provide one, the default settings file gets copied from $CCT_HOME/conf/project_settings.conf over to the project directory. cute of it honestly.
• -g, --config FILE — the configuration file. The default is to use the $CCT_HOME/conf/global_settings.conf file.
• -z, --map_size STRING — size of custom maps to create. For quickly generating new map sizes, use this option 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) provided will override the size(s) in the configuration files. obsessed with the flexibility ngl.
• -x, --start_at_xml — jump to XML generation. Skips performing blast, which can speed map generation if blast has already been done. This option is for creating new maps after making changes to the .conf files. ⚠️ Note that any changes in the .conf files related to blast will be ignored. yes, fr fr, ignored.
• -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). very "I already did the homework, just hand me the grade" energy.
• -f, --map_prefix STRING — prefix to be appended to map names (Default is to add no additional prefix).
• -b, --max_blast_comparisons INTEGER — the maximum number of BLAST results sets to be passed to the XML creation phase (Default is 100).
• -t, --sort_blast_tracks — sort BLAST results such that genomes with highest similarity are plotted first. bestie behaviour: best matches up front.
• --cct — colour BLAST results based on percent identity of hit instead of by source genome, and ignore use_opacity setting in configuration file.
• -m, --memory STRING — memory string to pass to Java's -Xmx option (Default is 1500m). feed the JVM, it's hungry 🍓
• -c, --custom STRINGS — settings used to customize the appearance of the map. this is your glow-up dial.
• -h, --help — show this message. the "hey, what does this do again" button 💀

🌈 EXAMPLE:

cgview_comparison_tool -p my_project -b 50 -t \
--custom tickLength=20 labelFontSize=15 --map_size medium,x-large

look at her go. literally iconic. 👑

💜 AUTHOR 💜

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

and that's the whole page, bestie — no notes, no cap, every flag accounted for 💖

kisses, bye! 💅✨ — this was cgview_comparison_tool version 20170919, dated August 2018. see u in the man pages 🦋