NOTE: For more information, use the unix "man" command:
cyrus% man mase
Also note that there is a mase manual available that lists all of the
functions avalialable in mase. However the following short notes will
save you much time in learning the basics of the mase editor.
Using mase to print out a PIMA alignment:
=========================================
Please note that in the following example, <Return> means hit the ENTER or
RETURN key on your keyboard.
Explanatory notes are enclosed in parenthesis ().
I. Starting up the mase editor:
mbcrr% mase <Return>
Read in a file? <Return>
name of file to read: filename.mase
II. Entering commands in mase.
SHIFT : (Hold down shift key while pressing colon key)
(You will now see command line. The command line in mase
is unique, you only have to type the first few characters of a
command, and mase will echo the full command on the
command line so that you don't have to type out the full
command names. You can also use arrow keys to select commands.)
III. Setting up your editing environment.
(If you use your right arrow key to see more of your sequence,
you will quickly find out that the first 25 positions of your
sequence window will remain fixed, and only the second window
of positions 26 to 50 will vary.
To remedy this problem you should enter the following commands
whenever you start up mase:)
After typing SHIFT :, type the following:
set
The command line will respond with SET VARIABLE
Hit a <Return>, and then type L
The command line will respond with LOCK WINDOWS
Type "ON" and Hit a <Return>
(Note: If your windows ever get out of synchronization,
you can reset them as follows:)
shift:
syn
The command line will respond with SYNCHRONIZE WINDOW
Hit a <Return>, then type the following:
ON
IV. EDITING YOUR MASE FILE.
A. Moving along current sequence
You can use the Right arrow or Left arrow to go to the
right or left. You can enter a number before the arrow
key to skip a certain amount of characters.
B. Inserting a gap character.
You can insert a gap character by typing i
You can delete a gap character with the delete key.
C. Moving to a different sequence.
Use the Up arrow or Down arrow.
D. Delete a sequence character.
IMPORTANT: By default, you can not delete any sequence
characters. If you wish to delete a sequence character, you
must enter the following commands:
SET VARIABLE PROTECT OFF
To initiate this command:
SHIFT :
Type SET V
The command line will respond with SET VARIABLE
Hit a <Return>, then type the following:
p
The command line will respond with "Set what -> Protect"
Hit a <Return>
The command line will respond with " Set to (boolean) -> OFF"
Hit a <Return>
E. Delete sequences (or patterns from a pima alignment.)
After typing SHIFT :, type the following:
ZAP
V. CHANGING MARGINS TO FIT ON 8 1/2" BY 11"
(Note, If you are off site and you want to change the width
of your mase output to make it more narrow so that it prints
on 8 1/2 by 11" paper, then do the following before entering
the "OUTPUT ALIGNED" command:)
After typing SHIFT :, type the following:
set
The command line will respond with SET VARIABLE
Hit a <Return>, then type the following:
O C and then press the DOWN ARROW once
The command line will respond with OUTPUT CHARACTERS PER LINE
Hit a <Return>, then delete 90 and enter 50
VI. Creating an output text file for publication:
(If you only have a few sequences, you can remove the form feed
characters so that your whole alignment can fit on one page.)
After typing SHIFT :, type the following:
set
The command line will respond with SET VARIABLE
Hit a <Return>, then type the following:
o u
The command line will respond with OUTPUT USE FORMFEED.
Hit a <Return>, then type:
off
VII. CREATING A TEXT OUTPUT FILE
After typing SHIFT :, type the following:
ou for "OUTPUT ALIGNED"
Hit a <Return>
Hit a <Return> for string mappings
Hit a <Return> for map colors
Now enter the name of your output file,
for example, peps.out
VIII. EXITING FROM MASE.
SHIFT :
q (TO QUIT)
y (TO CONFIRM QUITTING)
Your mase output file is in the file named "peps.out".
IX. SUMMARY OF USEFUL MASE COMMANDS:
To delete a whole sequence ZAP
to delete characters SET VARIABLE PROTECT OFF
to insert gaps i
multiple gaps 20i
X. FOR MORE HELP.
See the mase manual.
(Instead of calling mase directly, you can now run the shell script
"print-pima.sh" to output your pima alignment to a text file.)
For example:
mbcrr% print-pima.sh filename.pima > outfile
XI. Advanced Editing Commands.
Do delete complete domains amongst all of your sequences:
:Del Columns
Delete columns in which sequences -> 2-10
Delete at which column -> 402
Delete how many columns -> 20
To write out a whole domain section to a new file:
:Write Region to File
Save which sequences -> 2-10
Name of file to write -> tom1.temp
Start of region to save -> 1
End of region to save -> 99