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Top Forums Shell Programming and Scripting Passing arguments to interactive program through bash script, here document Post 302909556 by Corona688 on Thursday 17th of July 2014 02:42:48 PM
Old 07-17-2014
It already is taking it from a here document. Hopefully it should see no difference from this one to one in a script. Though -- I just found documentation for multalin here. It has a command-line mode which should be used instead of cramming input into it.

Code:
ma -c:/home/multalign/dna.tab -k:100.90 H_X.fas

Other options may be needed, I can't test this here, but here's a starting point. Get something that works when typed, then you should be able to script a loop around it.

If all else fails, you can use the here-document as above, but that's not really how it's intended to be used.

Last edited by Corona688; 07-17-2014 at 03:48 PM..
 

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SCRIPT(1)						    BSD General Commands Manual 						 SCRIPT(1)

NAME
script -- make typescript of terminal session SYNOPSIS
script [-akq] [-t time] [file [command ...]] DESCRIPTION
The script utility makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1). If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript. If the argument command is given, script will run the specified command with an optional argument vector instead of an interactive shell. The following options are available: -a Append the output to file or typescript, retaining the prior contents. -k Log keys sent to program as well as output. -q Run in quiet mode, omit the start and stop status messages. -t time Specify time interval between flushing script output file. A value of 0 causes script to flush for every character I/O event. The default interval is 30 seconds. The script ends when the forked shell (or command) exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-D (if ignoreeof is not set) for the C-shell, csh(1)). Certain interactive commands, such as vi(1), create garbage in the typescript file. The script utility works best with commands that do not manipulate the screen. The results are meant to emulate a hardcopy terminal, not an addressable one. ENVIRONMENT
The following environment variable is utilized by script: SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most shells set this variable automatically). SEE ALSO
csh(1) (for the history mechanism). HISTORY
The script command appeared in 3.0BSD. BUGS
The script utility places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. It is not possible to specify a command without also naming the script file because of argument parsing compatibility issues. When running in -k mode, echo cancelling is far from ideal. The slave terminal mode is checked for ECHO mode to check when to avoid manual echo logging. This does not work when in a raw mode where the program being run is doing manual echo. BSD
January 22, 2004 BSD
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