BLIXEMH(1)

💖 NAME 💖

blixemh — bestie, it displays multiple alignments against a reference sequence 💅✨

🦋 DESCRIPTION 🦋

Blixem — display multiple alignments against a reference sequence. That's the whole vibe, that's the assignment 👑

Okay so here's how you actually call her:

blixem [options] [<sequence_file>] <data_file> [X options]

Let me break down what's what, because the args are not interchangeable, bestie 🙈

• <sequence_file> holds the reference sequence, in FASTA format 🧬
• <data_file> is a GFF v3 file — it's carrying the alignments and other features ✨
• If you ghost <sequence_file> entirely (omitted, gone, not invited), then <data_file> has to bring the reference sequence itself, in FASTA format, sitting below a comment line that reads ##FASTA 📝

And the plot twist: both <sequence_file> and <data_file> can be swapped out for - to read from stdin (the pipe, the vibe pipeline 🚰). If <sequence_file> is the one getting piped, then heads up — the first line should have the sequence name and the second line has the sequence itself. Two lines. That's it. No cap. 💯

✨ Options ✨

• -t <type>, --display-type=<type> — MANDATORY 🚨 Like, you literally cannot skip this one. Are we in nucleotide mode or protein mode? Gotta pick. Must be one of:
  • N = nucleotide
  • P = protein
• -a <names>, --alignment-names=<names> — hand over a string with the names of the alignments, like "EST_mouse EST_human" etc. 🏷️
• -c <file>, --config-file=<file> — read configuration options from file ⚙️
• --abbrev-title-on — abbreviate window title prefixes ✂️
• --abbrev-title-off — do not abbreviate window title prefixes 🚫
• --compiled — show the package compile date 📅
• -d <data_file>, --data-file=<data_file> — another way of specifying <data_file>, this time as an argument 🫶
• --dataset — optional string to indicate a data-set that the alignments are from 📊
• -e <sequence_file>, --sequence-file=<sequence_file> — another way of specifying <sequence_file>, as an argument 🌸
• --dotter-first-match — calls Dotter on the first match to the right of the default start coord 🎯
• --fetch-server <nodeid:port> — makes Blixem pull sequences from a fetch server at machine nodeid on the given port (default 22100) 📡
• -h, --help — more detailed usage information, aka the lore drop 📖
• --hide-big-picture — hide the big picture section on start-up 🙈
• --hide-inactive-strand — hide the inactive strand (i.e. the reverse strand, or the forward strand if the -R option is used) 💤
• --highlight-diffs — turns on 'highlight differences' mode, where the mismatches get highlighted instead of the matches 👀✨
• --invert-sort — invert the sorting order 🔄
• -m <from[:to]>, --map-coords=<from[:to]> — remap the coordinate system so the given from coordinate maps to the given to coordinate (or to 1 if to isn't given) 🗺️
• -n, --negate-coords — when showing the reverse strand, negate the display coordinates ➖
• -o <n>, --offset=<n> — offset the reference sequence coordinate system by n 📐
• --optional-data — parse extra data like organism and tissue-type on start-up 🧫
• --remove-input-files — delete the input files after they've been parsed 🗑️
• -r, --reverse-strand — says that the given reference sequence is the reverse strand 🔃
• --save-temp-files — save any temporary files Blixem creates 💾
• --show-coverage — display the coverage section on start-up 📈
• --sort-mode=<mode> — default sort mode. Use the --help option to see the details 🔍
• --squash-matches — compress the alignment lists on start-up 🤏
• -s <n>, --start-coord=<n> — start with the display centred on coordinate n 🎯
• --start-next-match — start with the display centred on the first match to the right of the default start coord ➡️
• -y <file>, --styles-file=<file> — read color options from a key-value file. Use the --help option to see the details 🎨
• --version — show the package version number 🔢
• -z <start:end>, --zoom-range=<start:end> — set the initial range of coordinates to zoom the big picture in to 🔎
• --zoom-whole — start with the big picture zoomed all the way out so you can view the full reference sequence range 🌈

Also, some X options, because she contains multitudes:

• -acefont <font> — main font 🖋️
• -font <font> — menu font 🖋️

Heads up bestie: that --hide-inactive-strand note about the -R option is straight from the source, I'm just the messenger 💌

📜 The Lore (credits & legal) 📜

Written by Gemma Barson <gb10@sanger.ac.uk> 💖 Based on original code by Erik Sonnhammer <Erik.Sonnhammer@sbc.su.se> ✨

Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307. 📚

See http://www.sanger.ac.uk/resources/software/seqtools/ for more info 🌐

Copyright (c) 2009-2015: Genome Research Ltd. Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt ⚖️

Version 4.44.1 14:27:56 Oct 19 2017 ⏰

🌸 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 the whole page, bestie — blixemh 4.44.1, dated October 2017, and yes she ate 💅✨ no crumbs, periodt 🎀🦋