Program to display molecular sequence files using ncurses and a vim-like user interface. Meant to be an intermediate step between the Unix command line tools and graphical sequence editing programs. I find it useful when I'm logged into a server remotely and I want to look at some fasta files. It's a bit like samtools tview, but for sequence files (currently just FASTA and FASTQ format) instead of read alignments.

A single fasta file in codon mode:

Two files displayed at once, showing comparison mode:

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Requires the ncurses library to be installed. This means that seq_view will probably only work on UNIX-based systems.

To compile:

cd seq_view

g++ -o seq_view *.cpp -I"." -lncurses

Note that some systems may have ncurses installed as "curses." In that case compile with:

g++ -o seq_view *.cpp -I"." -lcurses

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seq_view FILE [FILE, FILE, ...]

At present, seq_view can only read FASTA and FASTQ files (more file formats may be added in the future). Use "-" to read from stdin.

Once the file is open, a set of keyboard commands, similar to vim's commands can be used to move through the data and control the appearance. To cancel any command type ESC. To quit use Ctrl-C or type 'q'.

q Close current window. When last window is closed, the program quits.

aq Close all windows and quit.

w Cycle through windows W Cycle through windows backwards

[number]w Move to window number (1 based)

All scrolling commands can be proceeded by a number that is multiplied by the current base scroll amount to get the number of positions to move.

[number]s Set base scroll amount to 10^[number]

[number]h Move [number] units to the left (can also use arrow keys)

[number]l Move [number] units to the right (can also use arrow keys)

[number]j Move [number] units down (can also use arrow keys)

[number]k Move [number] units up (can also use arrow keys)

K Move to the top

J Move to the bottom

G Move to the end [end]

g Move to the beginning [home]

[number]G Move to position [number]

c Turn on and off comparison highlighting. When comparison highlighting is on, sites that are all the same are highlighted. See section on comparison below.

[number]d Display mode. Right now has 1 for normal, 2 for codon, and three for ten. See display mode section below.

[number]n Adjust the number of characters of the names displayed to be [number].

[shift][left/right] Increase or decrease the number of characters of the names displayed.

[number]f Adjust the frame for codon display mode. Should be 1, 2, or 3.

These commands are entered by typing ";", similar to how vim commands are entered by typing ":". There are just a few of them right now:

"open": Type ";open FILENAME" to open FILENAME.

"mode": Type ";mode MODE" to switch display mode ("normal", "codon", or "ten" right now).

"compare-mode": Type ";compare-mode MODE" to switch between different ways of determining whether sites vary. See Comparison modes section below.

"bold": Toggle bolded sequence display. (Not working yet.)

"plain": Tests only whether all sequences have the same state, ignoring case.

"nucamb": Tests whether all sequences could be the same, taking into account IUPAC ambiguity codes and counting gaps ("-") as matching anything. For nucleotide sequences.

• normal Displays sequences with one column per base
• codon Puts a space between every codon (set the frame with 'f' key command).
• ten Puts a space every 10 bases