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how to replace spaces with '_' in a file?

 
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# 1  
Old 08-25-2010
how to replace spaces with '_' in a file?
Hello

#I have a file with a list of sequences; the sequence name is the line starting with '>'.
Code:
$cat infile

>AluYa5    SINE1/7SL    Homo sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtc
aggagatcgagaccatcccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg
>AluYb8    SINE1/7SL    Homo sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
tccgtctca
>AluYb9    SINE1/7SL    Homo sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc

#I would like to remove the spaces, the tabs , and '/' from the sequnce name and replace them with '_'.
Code:
$cat outfile

>AluYa5_SINE1_7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtc
aggagatcgagaccatcccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg
>AluYb8_SINE1_7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
tccgtctca
>AluYb9_SINE1_7SL_Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc

# 2  
Old 08-25-2010
Code:
sed "/^>/s/[ \t/]/_/g" file

# 3  
Old 08-25-2010
Quote:
Originally Posted by anbu23
Code:
sed "/^>/s/[ \t/]/_/g" file

it replaced only some:
Code:
sed "/^>/s/[ \t/]/_/g" infile.txt
>AluYa5    SINE1_7SL    Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggcggatcacgaggtc
aggagatcgagaccatcccggctaaaacggtgaaaccccgtctctactaaaaatacaaaaaattagccgg
>AluYb8    SINE1_7SL    Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc
tccgtctca
>AluYb9    SINE1_7SL    Homo_sapiens
ggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggccgaggcgggtggatcatgaggtc

are the spaces that were not replaced of a different kind?
# 4  
Old 08-25-2010
I just ran the command without any issues. What appears to be happening is that the tabs are not being replaced. What shell are you using? You might try replacing the double quotes with single quotes. I'd find it hard to believe, but it really looks like the \t is being treated as 'escape t' rather than a tab.

The other thing you could do, for testing, is replace the \t in the pattern with a real tab character and see if that makes any difference.

Very odd.
# 5  
Old 08-25-2010
Hi.

Both tr and sed worked for me:
Code:
#!/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

producing:
Code:
% ./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.

Best wishes ... cheers, drl
# 6  
Old 08-25-2010
Hi agama
How do I check which type of spaces I have in my file?
Also, can I send you my infile as an attachment so you can examine it?
I think when I do copy and paste the spaces change.
Thank you for your help

---------- Post updated at 05:22 PM ---------- Previous update was at 04:56 PM ----------
Quote:
Originally Posted by drl
Hi.

Both tr and sed worked for me:
Code:
#!/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

producing:
Code:
% ./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.

Best wishes ... cheers, drl

Hi drl
I am not sure how to use your code; can you give some simple steps for me to follow?
Thanks
# 7  
Old 08-25-2010
Rather than uploading your file, run this command and cut/paste the output:

Code:
head your-file-name-here | od -x -c

This should give us a better idea.

I'm guessing that using single quotes didn't work.
 
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