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Full Discussion: While loop with input in a bash script
Top Forums Shell Programming and Scripting While loop with input in a bash script Post 302957380 by faizlo on Saturday 10th of October 2015 12:52:02 AM
Old 10-10-2015
bash, tr, awk, sed
This is my master.sh script:
Code:
#!/bin/bash                                                                                             
#check to see if there is an input file:                                                                
if [ "$#" -lt 1 ]
then
  echo "Usage: $0 input_file ..."
  exit 1
fi

#Check if the file is empty or not                                                                      
file=$1
if [[ -s $1 ]]                   # if not empty:
then
  echo ""
  echo "**** $file has data."
  cat $1 | sed 's/>/\n>/g' > temp1.txt
  cat temp1.txt | sed '/^>/ d' > temp2.txt
  awk '!NF{if(++n <=1) print; next}; {n=0; print}' < temp2.txt > dna.out
  awk '/./{printf "%s",$0;next} {print "\n";} END{if (/./)print""}' dna.out > DNA.out
  echo "**** Number of DNA sequences:"
  grep -cve '^\s*$' DNA.out
  echo "**** Mumber of empty lines:"
  grep -ce '^\s*$' DNA.out
  echo ""
  #Remove duplicate empty lines:                                                                        
  awk '!NF{if(++n <=1) print; next}; {n=0; print}' < temp2.txt > DNA.out                               
  echo "**** DNA.out created (removed FASTA header)"
  #convert to mRNA and remove temp1, temp2 to avoid confusion                                           
  tr ACGT ACGU < DNA.out > RNA.out
  echo "**** RNA.out created (T -> U)"
  echo ""
  rm temp1.txt temp2.txt
  moved to conversion:                                                                                
  while read rna; do                                                                                  
      aawork=$(echo "${rna}" | sed -n -e 's/\(...\)\1 /gp' | sed -f rna.sed)                          
      echo "$aawork" | sed 's/ //g'                                                                   
      echo "$aawork" | tr ' ' '\012' | sort | sed '/^$/d' | uniq -c | sed 's/[ ]*\([0-9]*\) \(.*\)/\2\
: \1/'                                                                                                  
  done                                                                                                
  echo "**** creating AminoAcid from DNA:"
  ./convert_dna.sh < DNA.out > DNA_AminoAcid.out
  echo "**** Amino Acids from DNA saved in DAN_AminoAcid.out."
  echo "**** creating AminoAcid from RNA:"
  ./convert_rna.sh < RNA.out > RNA_AminoAcid.out
  echo "**** Amino Acids from RNA saved in RAN_AminoAcid.out."
  echo ""

else    # if the file is empty.                                                                         
  echo "**** $1 has no data, or file does not exist."
  echo "**** done!"
  echo ""
#clean the FASTA file and remove all lines starting with >, adding a new line first to avoid mixing all DNA samples:                                                                                           
fi;

convert_dna.sh and convert_rna.sh are two scripts that contain the while loop I mentioned in my first post. One with dna.sed and the other with rna.sed.

My question is how to add the while loop two times one with the dna.sed and the other one with rna.sed.
 

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LEARN ABOUT REDHAT

dos2unix

dos2unix(1)						      General Commands Manual						       dos2unix(1)

NAME

       dos2unix - DOS/MAC to UNIX text file format converter

SYNOPSYS

       dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

       [-hkqV] [--help] [--keepdate] [--quiet] [--version]

DESCRIPTION

       This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.

OPTIONS

       The following options are available:

       -h --help
	      Print online help.

       -k --keepdate
	      Keep the date stamp of output file same as input file.

       -q --quiet
	      Quiet mode. Suppress all warning and messages.

       -V --version
	      Prints version information.

       -c --convmode convmode
	      Sets conversion mode. Simulates dos2unix under SunOS.

       -o --oldfile file ...
	      Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.

       -n --newfile infile outfile ...
	      New  file  mode.	Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
	      used or you WILL lost your files.

EXAMPLES

       Get input from stdin and write output to stdout.

	      dos2unix

       Convert and replace a.txt. Convert and replace b.txt.

	      dos2unix a.txt b.txt

	      dos2unix -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.  Convert	c.txt  from  Mac  to  Unix
       ascii format.

	      dos2unix a.txt -c iso b.txt

	      dos2unix -c ascii a.txt -c iso b.txt

	      dos2unix -c mac a.txt b.txt

       Convert and replace a.txt while keeping original date stamp.

	      dos2unix -k a.txt

	      dos2unix -k -o a.txt

       Convert a.txt and write to e.txt.

	      dos2unix -n a.txt e.txt

       Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.

	      dos2unix -k -n a.txt e.txt

       Convert and replace a.txt. Convert b.txt and write to e.txt.

	      dos2unix a.txt -n b.txt e.txt

	      dos2unix -o a.txt -n b.txt e.txt

       Convert c.txt and write to e.txt. Convert and replace a.txt.  Convert and replace b.txt. Convert d.txt and write to f.txt.

	      dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt

DIAGNOSTICS

BUGS

       The program does not work properly under MSDOS in stdio processing mode.  If you know why is that so, please tell me.

AUTHORS

       Benjamin Lin - <blin@socs.uts.edu.au>

       Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>

MISCELLANY

       Tested environment:

	      Linux 1.2.0 with GNU C 2.5.8

	      SunOS 4.1.3 with GNU C 2.6.3

	      MS-DOS 6.20 with Borland C++ 4.02

       Suggestions and bug reports are welcome.

SEE ALSO

       unix2dos(1) mac2unix(1)

1995.03.31							   dos2unix v3.0						       dos2unix(1)
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