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I appreciate your help with this problem. I like to eliminate everything that is not a specific pattern from a string.
For example, below I like to eliminate everything that is not "5TTGTC".
But as seen here ^5TTGTC is not right. I used different combinations of ^(), ^{}, ^[], but none gave me what I am looking for. Appreciate your feedback!
echo ".,..,...+5TTGTC...+5TTGCC.+5TTGTC,,.,.,,.,+5ttgtc,.,,.,.+5TTGTC.+5TTGTC,..+5TTGTC" | sed 's/^5TTGTC//g'
Thanks in advance
You may use the following command if you want case sensitivity:
echo ".,..,...+5TTGTC...+5TTGCC.+5TTGTC,,.,.,,.,+5ttgtc,.,,.,.+5TTGTC.+5TTGTC,..+5TTGTC" | sed -r 's/(5TTGTC)|[,.A-Za-z+0-9]/\1/g'
The code above prints:
5TTGTC5TTGTC5TTGTC5TTGTC5TTGTC
The regular expression used above uses alternation to capture what you are interested in.
We match and capture what we are interested in (5TTGCC) and we match everything that is not the substring, in this case characters ,.A-Za-z+0-9.
You can check the behaviour of the regex here.
As pointed out by #EdMorton, the command can be simplified to:
echo ".,..,...+5TTGTC...+5TTGCC.+5TTGTC,,.,.,,.,+5ttgtc,.,,.,.+5TTGTC.+5TTGTC,..+5TTGTC" | sed -r 's/(5TTGTC)|./\1/g'
You can try this here.
For compatibility across sed versions the -r flag can be replaced by the -E flag.
You don't make it very clear what you are trying to achieve.
One way to get where you are trying to go could be the -o option in grep.
echo ".,..,...+5TTGTC...+5TTGCC.+5TTGTC,,.,.,,.,+5ttgtc,.,,.,.+5TTGTC.+5TTGTC,..+5TTGTC" | grep -o '5TTGTC'
Output:
5TTGTC
5TTGTC
5TTGTC
5TTGTC
5TTGTC
You can then change 5TTGTC into a pattern, e.g. grep -o '[0-9]TT[AG]GTC'
With any sed:
$ echo ".,..,...+5TTGTC...+5TTGCC.+5TTGTC,,.,.,,.,+5ttgtc,.,,.,.+5TTGTC.+5TTGTC,..+5TTGTC" |
sed 's/#//g; s/5TTGTC/#/g; s/[^#]//g; s/#/5TTGTC/g'
5TTGTC5TTGTC5TTGTC5TTGTC5TTGTC
With any awk:
$ echo ".,..,...+5TTGTC...+5TTGCC.+5TTGTC,,.,.,,.,+5ttgtc,.,,.,.+5TTGTC.+5TTGTC,..+5TTGTC" |
awk -v str='5TTGTC' '{gsub(str,"\n"); gsub(/[^\n]/,""); gsub(/\n/,str)}1'
5TTGTC5TTGTC5TTGTC5TTGTC5TTGTC
I got the following variable:
set location "America/New_York"
and want to display only the part before the / (slash) using fish shell syntax.
Expected result
America
Bash equivalent
Using bash, I was simply using a parameter expansion:
location="America/New_York"
echo ${location##*/}"
Question
How do I do that in a fish-way?
Since fish 2.3.0, there's a builtin called string that has several subcommands including replace, so you'll be able to do
string replace -r "/.*" "" -- $location
or
set location (string split "/" -- $location)[1]
See http://fishshell.com/docs/current/commands.html#string.
Alternatively, external tools like cut, sed or awk all work as well.
A possible solution is to use cut but, that look hackish:
set location "America/New_York"
echo $location|cut -d '/' -f1
America
Use the field selector -f of string split
> string split / "America/New_York" -f1
America
and accordingly:
set location (string split / "America/New_York" -f1)
Sidenote: For the latter string involving multiple slashes, I don't know anything better than the cumbersome -r -m1 -f2:
> string split / "foo/bar/America/New_York" -r -m1 -f2
New_York
I have a bash script in which I have a few qsubs. Each of them are waiting for a preivous qsub to be done before starting.
My first qsub consist of sending files in a certain directory to a perl program and having the outfiles printed in a new directory. At the end, I echo the array with all my jobs names. This script works as intented.
mkdir -p /perl_files_dir
for ID_FILES in `ls Infiles_dir/*.txt`;
do
JOB_ID=`echo "perl perl_scirpt.pl $ID_FILES" | qsub -j oe `
JOB_ID_ARRAY="${JOB_ID_ARRAY}:$JOB_ID"
done
echo $JOB_ID_ARRAY
My second qsub is meant to sort all my previous files made with my perl script in a new outfile and to start after all these jobs are done (about 100 jobs) with depend=afterany. Again, this part is working fine.
SORT_JOB=`echo "sort -m -n perl_files_dir/*.txt >>sorted_file.txt" | qsub -j oe -W depend=afterany$JOB_ID_ARRAY`
SORT_ARRAY="${SORT_ARRAY}:$SORT_JOB"
My issue is that in my sorted file, I have a few columns I wish to remove (2 to 6), so I came up with this last line using awk piped to sed with another depend=afterany
SED=`echo "awk '{\$2="";\$3="";\$4="";\$5="";\$6=""; print \$0}' sorted_file.txt \
| sed 's/ //g' >final_file.txt" | qsub -j oe -W depend=afterany$SORT_ARRAY`
This last step creates final_file.txt, but leaves it empty. I added SED= before my echo because it would otherwise give me Command not found.
I tried without the pipe so it would just print everything. Unfortunately it prints nothing.
I assume it is not opening my sorted file and this is why my final file is empty after my sed. If it's the case, then why won't awk read it?
In my script, I am using variables to define my directories and files (with the correct path). I know my issue is not about find my files or directories since they are perfectly defined at the beginning and used throughout the script. I tried to write the whole path instead of a variable and I get the same results.
for ID_FILES in `ls Infiles_dir/*.txt`
Simplify this to
for ID_FILES in Infiles_dir/*.txt
ls lists the files you pass it (except when you pass it directories, then it lists their content). Rather than telling it to display a list of files and parse the output, use the list of files you already have! This is more reliable (parsing the output of ls will fail if the file names contain whitespace or wildcard characters), clearer and faster. Don't parse the output of ls.
SORT_JOB=`echo "sort -m -n perl_files_dir/*.txt >>sorted_file.txt" | qsub -j oe -W depend=afterany$JOB_ID_ARRAY`
You'd make your life simpler if you used the right form of quoting in the right place. Don't use backquotes, because it's difficult to know how to quote things inside. Use $(…) instead, it's exactly equivalent except that it is parsed in a sane way.
I recommend using a here document for the shell snippet that you're feeding to qsub. You have fewer quoting issues to worry about, and it's more readable.
While we're at it, always put double quotes around variable substitutions and command substitutions: "$some_variable", "$(some_command)". Annoyingly, $var in shell syntax doesn't mean “take the value of the variable var”, it means “take the value of the variable var, parse it as a list of wildcard patterns, and replace each pattern by the list of matching files if there are matching files”. This extra stuff is turned off if the substitution happens inside double quotes (or in a here document, by the way): "$var" means “take the value of the variable var”.
SORT_JOB=$(qsub -j oe -W depend="afterany$JOB_ID_ARRAY" <<'EOF'
sort -m -n perl_files_dir/*.txt >>sorted_file.txt
EOF
)
We now get to the snippet where the quoting was actually causing a problem.
SED=`echo "awk '{\$2="";\$3="";\$4="";\$5="";\$6=""; print \$0}' sorted_file.txt \
| sed 's/ //g' >final_file.txt" | qsub -j oe -W depend=afterany$SORT_ARRAY`
The string that becomes the argument to the echo command is:
awk '{$2=;$3=;$4=;$5=;$6=; print $0}' sorted_file.txt | sed 's/ //g' >final_file.txt
This is syntactically incorrect, and that's why you're not getting any output.
You didn't escape the double quotes inside what was meant to be the awk snippet. It's a lot clearer if you use a here document. Also, you don't need the SED= part. You added it because you had a command substitution (a command between …), which substitutes the output of a command. But since you aren't interested in the output of the qsub command, don't take its output, just execute it.
qsub -j oe -W depend="afterany$SORT_ARRAY" <<'EOF'
awk '{$2="";$3="";$4="";$5="";$6=""; print $0}' sorted_file.txt |
sed 's/ //g' >final_file.txt
EOF
I'm not familiar with qsub, but presumably there's a way to get the error output and the return status of the commands it runs. Inspect that error output, you should have seen the errors from awk.
The version of awk that I am using, does not like the character escapes
awk --version
GNU Awk 3.1.7
spuder#cent64$ awk '{\$2="";\$3="";\$4=""; print \$0}' foo.txt
awk: {\$2="";\$3="";\$4=""; print \$0}
awk: ^ backslash not last character on line
Try the following syntax
awk '{for(i=2;i<=7;i++) $i="";print}' foo.txt
As a side note, if you are using Torque 4.x you may not be able to use a comma separated list of jobs with -W depend=, instead you may need to create a new PBS declarative (-W) for each job.
eg...
#Invalid syntax in newer versions of torque
qsub -W depend=foo,bar
Resources
backslash in gawk fields
Print all but the first three columns
http://docs.adaptivecomputing.com/torque/help.htm#topics/commands/qsub.htm#-W
We have a process which can use a file containing sed commands to alter piped input.
I need to replace a placeholder in the input with a variable value, e.g. in a single -e type of command I can run;
$ echo "Today is XX" | sed -e "s/XX/$(date +%F)/"
Today is 2012-10-11
However I can only specify the sed aspects in a file (and then point the process at the file), E.g. a file called replacements.sed might contain;
s/XX/Thursday/
So obviously;
$ echo "Today is XX" | sed -f replacements.sed
Today is Thursday
If I want to use an environment variable or shell value, though, I can't find a way to make it expand, e.g. if replacements.txt contains;
s/XX/$(date +%F)/
Then;
$ echo "Today is XX" | sed -f replacements.sed
Today is $(date +%F)
Including double quotes in the text of the file just prints the double quotes.
Does anyone know a way to be able to use variables in a sed file?
This might work for you (GNU sed):
cat <<\! > replacements.sed
/XX/{s//'"$(date +%F)"'/;s/.*/echo '&'/e}
!
echo "Today is XX" | sed -f replacements.sed
If you don't have GNU sed, try:
cat <<\! > replacements.sed
/XX/{
s//'"$(date +%F)"'/
s/.*/echo '&'/
}
!
echo "Today is XX" | sed -f replacements.sed | sh
AFAIK, it's not possible. Your best bet will be :
INPUT FILE
aaa
bbb
ccc
SH SCRIPT
#!/bin/sh
STRING="${1//\//\\/}" # using parameter expansion to prevent / collisions
shift
sed "
s/aaa/$STRING/
" "$#"
COMMAND LINE
./sed.sh "fo/obar" <file path>
OUTPUT
fo/obar
bbb
ccc
As others have said, you can't use variables in a sed script, but you might be able to "fake" it using extra leading input that gets added to your hold buffer. For example:
[ghoti#pc ~/tmp]$ cat scr.sed
1{;h;d;};/^--$/g
[ghoti#pc ~/tmp]$ sed -f scr.sed <(date '+%Y-%m-%d'; printf 'foo\n--\nbar\n')
foo
2012-10-10
bar
[ghoti#pc ~/tmp]$
In this example, I'm using process redirection to get input into sed. The "important" data is generated by printf. You could cat a file instead, or run some other program. The "variable" is produced by the date command, and becomes the first line of input to the script.
The sed script takes the first line, puts it in sed's hold buffer, then deletes the line. Then for any subsequent line, if it matches a double dash (our "macro replacement"), it substitutes the contents of the hold buffer. And prints, because that's sed's default action.
Hold buffers (g, G, h, H and x commands) represent "advanced" sed programming. But once you understand how they work, they open up new dimensions of sed fu.
Note: This solution only helps you replace entire lines. Replacing substrings within lines may be possible using the hold buffer, but I can't imagine a way to do it.
(Another note: I'm doing this in FreeBSD, which uses a different sed from what you'll find in Linux. This may work in GNU sed, or it may not; I haven't tested.)
I am in agreement with sputnick. I don't believe that sed would be able to complete that task.
However, you could generate that file on the fly.
You could change the date to a fixed string, like
__DAYOFWEEK__.
Create a temp file, use sed to replace __DAYOFWEEK__ with $(date +%Y).
Then parse your file with sed -f $TEMPFILE.
sed is great, but it might be time to use something like perl that can generate the date on the fly.
To add a newline in the replacement expression using a sed file, what finally worked for me is escaping a literal newline. Example: to append a newline after the string NewLineHere, then this worked for me:
#! /usr/bin/sed -f
s/NewLineHere/NewLineHere\
/g
Not sure it matters but I am on Solaris unix, so not GNU sed for sure.
I'd like to use Sed to expand variables inside a file.
Suppose I exported a variable VARIABLE=something, and have a "test" file with the following:
I'd like to expand this: "${VARIABLE}"
I've been trying commands like the following, but to no avail:
cat test | sed -e "s/\(\${[A-Z]*}\)/`eval "echo '\1'"`/" > outputfile
The result is the "outputfile" with the variable still not expanded:
I'd like to expand this: "${VARIABLE}"
Still, running eval "echo '${VARIABLE}' in bash console results in the value "something" being echoed. Also, I tested and that pattern is trully being matched.
The desired output would be
I'd like to expand this: "something"
Can anyone shed a light on this?
Consider your trial version:
cat test | sed -e "s/\(\${[A-Z]*}\)/`eval "echo '\1'"`/" > outputfile
The reason this doesn't work is because it requires prescience on the part of the shell. The sed script is generated before any pattern is matched by sed, so the shell cannot do that job for you.
I've done this a couple of ways in the past. Normally, I've had a list of known variables and their values, and I've done the substitution from that list:
for var in PATH VARIABLE USERNAME
do
echo 's%${'"$var"'}%'$(eval echo "\$$var")'%g'
done > sed.script
cat test | sed -f sed.script > outputfile
If you want to map variables arbitrarily, then you either need to deal with the whole environment (instead of the fixed list of variable names, use the output from env, appropriately edited), or use Perl or Python instead.
Note that if the value of an environment variable contains a slash in your version, you'd run into problems using the slash as the field separator in the s/// notation. I used the '%' since relatively few environment variables use that - but there are some found on some machines that do contain '%' characters and so a complete solution is trickier. You also need to worry about backslashes in the value. You probably have to use something like '$(eval echo "\$$var" | sed 's/[\%]/\\&/g')' to escape the backslashes and percent symbols in the value of the environment variable. Final wrinkle: some versions of sed have (or had) a limited capacity for the script size - older versions of HP-UX had a limit of about 100. I'm not sure whether that is still an issue, but it was as recently as 5 years ago.
The simple-minded adaptation of the original script reads:
env |
sed 's/=.*//' |
while read var
do
echo 's%${'"$var"'}%'$(eval echo "\$$var" | sed 's/[\%]/\\&/g')'%g'
done > sed.script
cat test | sed -f sed.script > outputfile
However, a better solution uses the fact that you already have the values in the output from env, so we can write:
env |
sed 's/[\%]/\\&/g;s/\([^=]*\)=\(.*\)/s%${\1}%\2%/' > sed.script
cat test | sed -f sed.script > outputfile
This is altogether safer because the shell never evaluates anything that should not be evaluated - you have to be so careful with shell metacharacters in variable values. This version can only possibly run into any trouble if some output from env is malformed, I think.
Beware - writing sed scripts with sed is an esoteric occupation, but one that illustrates the power of good tools.
All these examples are remiss in not cleaning up the temporary file(s).
Maybe you can get by without using sed:
$ echo $VARIABLE
something
$ cat test
I'd like to expand this: ${VARIABLE}
$ eval "echo \"`cat test`\"" > outputfile
$ cat outputfile
I'd like to expand this: something
Let shell variable interpolation do the work.