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Full Discussion: Passing arguments to interactive program through bash script, here document
Top Forums Shell Programming and Scripting Passing arguments to interactive program through bash script, here document Post 302909549 by biochemist on Thursday 17th of July 2014 02:26:10 PM
Old 07-17-2014
Dear Corona688,
Below the word by word execution of program from terminal: I have the executable set in the path:

Code:
[host@localhost temp]$ ma
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

Sequence file:  H_X.fas

Input format (gcg, mul, embl, genbank, auto): (def = auto)  auto

Other Input parameters (y/n) ?: (def=n) n

Symbol comparison table: (def = blosum62.tab) /home/multalign/dna.tab

Gap value ? (def = value in Symbol comparison file):   

Other Alignment parameters (y/n) ?: (def=n) n

Output format (msf, mul, doc): (def = msf) msf

Other Output parameters (y/n) ?: (def=n) y

Ouput order as (aligned, input)) ?: (def=aligned) aligned

Save cluster as a drawing or as a list (d/l) ?: (def = l) l

 Consensus levels (default = 90 and 50) ? :  100.90
Reading H_X.fas
Sequence #  26
Reading /home/multalign/dna.tab
Saving Configuration.
Clustering with fast
Action successful                                                              
Saving H_X.clu
Aligning
gnl|hbvcds|AB059659_ ..................with gnl|hbvcds|EF157291_ Position #    gnl|hbvcds|AB059659_ ...................with gnl|hbvcds|EU498228_ Position #   gnl|hbvcds|AB059659_ ....................with gnl|hbvcds|FJ356715_ Position #  gnl|hbvcds|AB059659_ .....................with gnl|hbvcds|FJ356716_ Position # gnl|hbvcds|AB059659_ ......................with gnl|hbvcds|HM066946_ Position #gnl|hbvcds|AB059659_ .......................with gnl|hbvcds|HM117850_ Position gnl|hbvcds|AB059659_ ........................with gnl|hbvcds|HM117851_ Positiongnl|hbvcds|AB179747_ ................with gnl|hbvcds|AB059660_ ..Position #    gnl|hbvcds|AB059660_ ...................with gnl|hbvcds|AB059659_ Position #   gnl|hbvcds|AB059659_ ....................with gnl|hbvcds|AB205010_ Position #  gnl|hbvcds|AB059659_ .....................with gnl|hbvcds|HM117851_ Position # gnl|hbvcds|AB059659_ ......................with gnl|hbvcds|AB064315_ Position #gnl|hbvcds|AB059659_ .......................with gnl|hbvcds|AY090454_ .PositionAction successful  2 iteration(s)                                              
Saving H_X.cl2
Saving H_X.msf
[host@localhost temp]$

Above options comes up when trying to execute the program from terminal. I am trying to run this program automatically so that I don't have to do this interactively for 1000 of sequences.

I really appreciate your time and response Corona688.
Regards
 

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LEARN ABOUT DEBIAN

fastacmd

FASTACMD(1)						     NCBI Tools User's Manual						       FASTACMD(1)

NAME

       fastacmd - retrieve FASTA sequences from a BLAST database

SYNOPSIS

       fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t]

DESCRIPTION

       fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option.  An example fastacmd call would be

								fastacmd -d nr -s p38398

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -D N   Dump the entire database in some format:
	      1      fasta
	      2      GI list
	      3      Accession.version list

       -I     Print database information only (overrides all other options)

       -L start,stop
	      Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence)

       -P N   Retrieve sequences with Protein Identification Group (PIG) N.

       -S N   Strand on subsequence (nucleotide only):
	      1      top (default)
	      2      bottom

       -T     Print taxonomic information for requested sequence(s)

       -a     Retrieve duplicate accessions

       -c     Use ^A (01) as non-redundant defline separator

       -d str Database (default is nr)

       -i str Input file with GIs/accessions/loci for batch retrieval

       -l N   Line length for sequence (default = 80)

       -o filename
	      Output file (default = stdout)

       -p type
	      Type of file:
	      G      guess (default): look for protein, then nucleotide
	      T      protein
	      F      nucleotide

       -s str Comma-delimited search string(s).  GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'

       -t     Definition line should contain target GI only

EXIT STATUS

	      0      Completed successfully.
	      1      An error (other than those below) occurred.
	      2      The BLAST database was not found.
	      3      A search (accession, GI, or taxonomy info) failed.
	      4      No taxonomy database was found.

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       blast(1), /usr/share/doc/blast2/fastacmd.html.

NCBI
								    2005-11-04							       FASTACMD(1)
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