#!/usr/bin/env bash

# @(#) s1    Demonstrate replacement with tr or sed.

# Infrastructure details, environment, commands for forum posts. 
# Uncomment export command to run script as external user.
# export PATH="/usr/local/bin:/usr/bin:/bin"
set +o nounset
pe() { for i;do printf "%s" "$i";done; printf "\n"; }
pl() { pe;pe "-----" ;pe "$*"; }
LC_ALL=C ; LANG=C ; export LC_ALL LANG
pe ; pe "Environment: LC_ALL = $LC_ALL, LANG = $LANG"
pe "(Versions displayed with local utility \"version\")"
c=$( ps | grep $$ | awk '{print $NF}' )
version >/dev/null 2>&1 && s=$(_eat $0 $1) || s=""
[ "$c" = "$s" ] && p="$s" || p="$c"
version >/dev/null 2>&1 && version "=o" $p printf specimen tr sed
set -o nounset
pe

FILE=${1-data1}

# Display sample of data file, with head & tail as a last resort.
pe " || start [ first:middle:last ]"
specimen $FILE \
|| { pe "(head/tail)"; head -n 5 $FILE; pe " ||"; tail -n 5 $FILE; }
pe " || end"

pl " Results with tr or sed [both worked]:"
# 'SPACETAB/'
# sed -r 's|[     /]+|_|g' $FILE |
tr -s '     /' '_' < $FILE |
tee t1

# Check results.

pl " Comparison with desired results:"
if [ ! -f expected-output.txt -o ! -s expected-output.txt ]
then
  pe " Comparison file \"expected-output.txt\" zero-length or missing."
  exit
fi
if cmp expected-output.txt t1
then
  pe " Passed -- files have same content."
else
  pe " Failed -- files not identical -- detailed comparison follows."
  if diff -b expected-output.txt t1
  then
    pe " Passed by ignoring whitespace differences."
  fi
fi

exit 0

% ./s1

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
OS, ker|rel, machine: Linux, 2.6.26-2-amd64, x86_64
Distribution        : Debian GNU/Linux 5.0 
GNU bash 3.2.39
printf - is a shell builtin [bash]
specimen (local) 1.17
tr (GNU coreutils) 6.10
GNU sed version 4.1.5

 || start [ first:middle:last ]
Whole: 5:0:5 of 8 lines in file "data1"
>AluYa5    SINE1/7SL    Homo sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtc
aggagatcgagaccatcccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg
>AluYb8    SINE1/7SL    Homo sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
tccgtctca
>AluYb9    SINE1/7SL    Homo sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
 || end

-----
 Results with tr or sed [both worked]:
>AluYa5_SINE1_7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtc
aggagatcgagaccatcccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg
>AluYb8_SINE1_7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
tccgtctca
>AluYb9_SINE1_7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc

-----
 Comparison with desired results:
 Passed -- files have same content.