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Top Forums Shell Programming and Scripting Passing arguments to interactive program through bash script, here document Post 302909537 by biochemist on Thursday 17th of July 2014 01:38:01 PM
Old 07-17-2014
Dear Corona688,
Thank you for your reply. I incorporated the changes but it seems its not able to find the data file ( although i put explicit path name).
Below is the code and error:
Code:
#!/bin/bash                                                                  

cat <<EOF > data.txt                                                         
auto                                                                         
n                                                                            
/home/multalign/tab/dna.tab                                           
                                                                             
n                                                                            
msf                                                                          
y                                                                            
aligned                                                                      
                                                                             
100.90                                                                       
EOF                                                                          

#for x in {A..H}                                                             
for x in H
do
    echo $x
    for y in PreS1 PreS2 S X
    do
        /home/multalign/tab/ma ${x}_${y}.fas < data.txt
        echo Done: ${x}_${y}.fas
    done
done

Error:
Code:
H
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_PreS1.fas
Sequence #  30

Error: Error reading blosum62.tab. 
Done: H_PreS1.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_PreS2.fas
Sequence #  30

Error: Error reading blosum62.tab. 
Done: H_PreS2.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_S.fas
Sequence #  72

Error: Error reading blosum62.tab. 
Done: H_S.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_X.fas
Sequence #  26

Error: Error reading blosum62.tab. 
Done: H_X.fas

Thanks
 

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SCRIPT(1)							   User Commands							 SCRIPT(1)

NAME
script - make typescript of terminal session SYNOPSIS
script [options] [file] DESCRIPTION
script makes a typescript of everything displayed 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 the dialogue in this file. If no filename is given, the dialogue is saved in the file type- script. OPTIONS
-a, --append Append the output to file or to typescript, retaining the prior contents. -c, --command command Run the command rather than an interactive shell. This makes it easy for a script to capture the output of a program that behaves differently when its stdout is not a tty. -e, --return Return the exit code of the child process. Uses the same format as bash termination on signal termination exit code is 128+n. -f, --flush Flush output after each write. This is nice for telecooperation: one person does `mkfifo foo; script -f foo', and another can supervise real-time what is being done using `cat foo'. --force Allow the default output destination, i.e. the typescript file, to be a hard or symbolic link. The command will follow a symbolic link. -q, --quiet Be quiet (do not write start and done messages to standard output). -t[file], --timing[=file] Output timing data to standard error, or to file when given. This data contains two fields, separated by a space. The first field indicates how much time elapsed since the previous output. The second field indicates how many characters were output this time. This information can be used to replay typescripts with realistic typing and output delays. -V, --version Display version information and exit. -h, --help Display help text and exit. NOTES
The script ends when the forked shell exits (a control-D for 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. script works best with commands that do not manipulate the screen, the results are meant to emulate a hardcopy terminal. It is not recommended to run script in non-interactive shells. The inner shell of script is always interactive, and this could lead to unexpected results. If you use script in the shell initialization file, you have to avoid entering an infinite loop. You can use for example the .profile file, which is read by login shells only: if test -t 0 ; then script exit fi You should also avoid use of script in command pipes, as script can read more input than you would expect. 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), scriptreplay(1) HISTORY
The script command appeared in 3.0BSD. BUGS
script places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. script is primarily designed for interactive terminal sessions. When stdin is not a terminal (for example: echo foo | script), then the session can hang, because the interactive shell within the script session misses EOF and script has no clue when to close the session. See the NOTES section for more information. AVAILABILITY
The script command is part of the util-linux package and is available from Linux Kernel Archive <https://www.kernel.org/pub/linux/utils /util-linux/>. util-linux June 2014 SCRIPT(1)
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