Passing arguments to interactive program through bash script, here document Post: 302909537

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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

07-17-2014

Registered User

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

biochemist

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LEARN ABOUT DEBIAN

bp_sreformat

BP_SREFORMAT(1p)					User Contributed Perl Documentation					  BP_SREFORMAT(1p)

NAME

       bpsreformat - convert sequence formats

DESCRIPTION

       This script uses the SeqIO system that allows conversion of sequence formats either sequence data or multiple sequence alignment data.  The
       name comes from the fact that Sean Eddy's program sreformat (part of the HMMER pkg) already does this.  Sean's program tries to guess the
       input formats while in our code we currently require your to specify what the input and output formats are and if the data is from a
       multiple sequence alignment or from straight sequence files.

       Usage:

       bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT

	 -h/--help	  Print this help

	 -if/--informat   Specify the input format

	 -of/--outformat  Specify the output format

	 -i/--input	  Specify the input file name
			  (to pass in data on STDIN use minus sign as filename)
	 -o/--output	  Specify the output file name
			  (to pass data out on STDOUT use minus sign as filename)

	 --msa		  Specify this is multiple sequence alignment data

	 --special	  Will pass on special parameters to the AlignIO/SeqIO
			  object -- most of these are for Bio::AlignIO objects
			  Comma separated list of the following
			  nointerleaved   -- for phylip,non-interleaved format
			  idlinebreak	  -- for phylip, makes it molphy format
			  percentages	  -- for clustalw, show % id per line

perl v5.14.2							    2012-03-02							  BP_SREFORMAT(1p)

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