How To Run A Command In Another Command?

hi guys

i am trying to find the "size" of a "block" of data in LARGE data files, the example below test_data.txt is very simplified. by "size" i mean the difference in line numbers of a block, and the "size" will be constant throughout the file so

1234 6.600000 4321
1234 8.500000 4321
1234 1.800000 4321
1234 2.300000 4321
1234 8.500000 4321
1234 2.800000 4321

if i define a block as whenever i find 8.500000 in the second column, then in the example the the block size would be 3 becasue 8.500000 occurs on the 5th line and on the 2nd. right now i am using

Code:

 grep -n "8.500000" test_data.txt | cut -f1 -d:

and/or

Code:

 awk '/8.500000/ {print FNR}' test_data.txt

obviously i don't remeber how to tag text as code?

btw, the grep command is much much faster

both of these commands give an entire list (long list of number for files greater than a gig) of line numbers which i then have to subtract one from another to come up with 3 in the example. not that i'm opposed to doing math, but i would think awk or grep should be able to do this for me

ideas?

tabby

Hi Forum members,

I'm interested to get the date on which particular command was ran.

I've below in my .bashrc

Code:

export HISTTIMEFORMAT="%d/%m/%y %T "

I ran history | grep "cp" | less

I get an output like:

Quote:
1288 27/05/15 09:12:55 sacct -j 767151 --format=elapsed,ncpus,state
27/05 is today's date. But I'm interested for the date, the above output was ran.

What am I missing?

Hey guys,

Something is puzzling me!

I saw someone use the grep in the following way and I'm not sure I understand what it does, and if there's any benefit to using it this way.

Code:

grep X.X.X.X /var/log/log.log | grep -v query

I checked the man file which confirmed that -v is relating to matching non grouping lines (which I'm not sure I fully understand either!) but I don't see any difference in the output of the above command versus the same command without the | grep -v query bit..

Why would you pipe grep into grep unless you were searching for something specific within the search results?

Does query mean something else?

Hi All,
How can I replace the particular word using sed or awk
Code:

$ BUGZILLAURL="https://mylocalserver.com/bugzilla"
$ PROJECTNAME="mybugs"
$ echo "$BUGZILLAURL/$PROJECTNAME" 
https://mylocalserver.com/bugzilla/mybugs

There is a urlbase line in data/params file which has an empty variable, pls see 2nd line from below command's output.
Code:

$ grep -i "urlbase" data/params 
           'docs_urlbase' => 'docs/%lang%/html/',
           'urlbase' => '',
           'webdotbase' => 'http://www.research.att.com/~north/cgi-bin/webdot.cgi/%urlbase%',

Or search only for that line which I wanted to be as 'urlbase' => 'https://mylocalserver.com/bugzilla/mybugs',
Code:

$ grep -i "'urlbase'" data/params 
           'urlbase' => '',

So expecting your kind help to replace '' word with 'https://mylocalserver.com/bugzilla/mybugs' using sed or awk.

Thanks.

Hi ,

Please explain what the below command means ..


Code:

if grep -c -i Y $INIFILE > /dev/null

I know what is the use of grep, it is used for finding a character or string in a file. But i could not understand the above form of grep command.

I am new to linux so this might be a simple question, but please throw some light on it.


Edited

And also please explain why they are creating a file in null in the below command

Code:

cat /dev/null > $DATA_DIR/$DATAFILE

Hi all,

I'm trying to identify files that do not have matches for certain strings. FYI, these are files of DNA sequences and I'm trying to find those that are NOT sampled for any species by my group of interest (e.g., genes that are specific to that group of organisms).

I tried this code but it's actually yielding a list of files that DO match for my regexp.
Code:

for FILENAME in *.fas
do
grep -q -L ">PBAH" $FILENAME && grep -q -L ">SKOW" $FILENAME && grep -q -L ">CGRA" $FILENAME && echo $FILENAME
done

Basically I want to somehow go through and file files that do not contain ">PBAH" ">SKOW" or ">CGRA". Any assistance would be greatly appreciated!

Best,
Kevin

Dear forum of Linux,
could I output a list of five books with their filename titles into one file?
In order o output all the contents of all the files with their filenames there was: find . -type f | while read x; echo -e "\n$x";cat "$x";done > бетховен.txt

In spite of them being successively named 1Atitle... 2Atitle the two first aren't 1A 2A, but 1A ..5A (2
3 4) They actually a 1АБетховен.. 5АБетховен... It now breaks all things I hoped.

Could the task be done by head, cat or grep command? Cat has no filename parameter, head can't output the whole file and grep has a filename parameter but it's primary use is searching one line. In find I coulnd't write each file by hand ...

i've got another command awk '{ print FILENAME, $0 }' (it claims to show the filename though it shows it didn't end


Currently I blame the Linux learning curve because of google results and non-answered messages and all that after translation if a nice question directly to English. Isn't that it hard to make more help to design unixes language in that way to be really descriptive and write it as you think.
I'm deeply sorry for that grief!...(

If there is one Windows XP feature that I greatly miss in Mint, it is the Search Companion.

I have been struggling with 'grep' in order to create something suitable but with limited success. Take the following problem:-

I wish to interrogate the folder home/dell/Documents/Domestic/Recipes, searching for all files containing the word "mushroom" or "mushrooms", ignoring case. (I can manage the latter. )

Each individual file search should terminate at the first instance of a match and move to the next file. (Recursive, yeh?) Only the file names need to be listed and the output should be paged to allow for easier reading of long lists.

Several different types of file may be involved, including .doc, .odt, .txt .pdf, .htm and .rtf. It would be nice to include all of them in one command. (Wild card behaviour in grep is not entirely predictable - at least not for me.) Running a separate grep command for each different file type would be tedious.

A significant difficulty is that, if grep fails with a syntax, or run-time error, it generally reports the fact but it also has a habit of producing no output, perhaps not returning to the command prompt, whilst sitting inviting the user to decide what to do next. What makes this particularly frustrating is that some file types might not be amenable to a grep search. Text in .txt files and, it would appear, .doc files appears to be searchable but I suspect that .odt files might be more problematic. The snag in such circumstances is trying to interpret grep's response. Does a null return mean that no match was found or that the file format cannot be successfully interrogated? Such failure might not be apparent if the associated file names are simply excluded from the output list.

Apart from grep, is there any other software that would do the job? Sadly LibreOffice Writer seems to be lacking in this area.

I'm currently using the command below, to output the memory usage of a debian system in bash scripts.

Code:

memusage=$(memusage=$(/usr/bin/free | grep Mem | awk '{print $3/$2 * 100.0 "%"}' | cut -d "%" -f1);echo "$(printf "%0.0f\n" $memusage)") && echo Memory Usage is $memusage

Being new to Linux though, I just found out that Linux takes up a lof of memory and puts it in cached.

Code:

root@Client1:~# free -m
             total       used       free     shared    buffers     cached
Mem:           927        799        128          0         15        754
-/+ buffers/cache:         28        898
Swap:           99          0         99

So the first command will actually output that the memory usage is 87%, when in reality is not. Its actually thinking that the memory usage is high because its also counting the cached memory, as used memory.

How can I modify the first command not to consider cached memory, as used memory?

Thanks

Hi all,

Been reading on stdin, stdout and stderr and encounter 2 questions, hope gurus here can advise.

0 = stdin
1 = stdout
2 = stderr

Code:

Sun Dec 21 03:53:42 SGT 2014 > cat test5.sh
#!/bin/bash

echo "Please enter value for name :"
read name
echo "Your name is $name."

echo "Next echo will be a syntax error"
ehco

Code:

Sun Dec 21 03:53:46 SGT 2014 > test5.sh 1> output.txt 2> error.txt
Noob

Sun Dec 21 03:54:56 SGT 2014 > cat output.txt
Please enter value for name :
Your name is Noob.
Next echo will be a syntax error

Sun Dec 21 03:55:23 SGT 2014 > cat error.txt
/home/alan/scripts/test5.sh: line 8: ehco: command not found
Sun Dec 21 03:55:26 SGT 2014 >

Which so far all is good and the correct way to output everything including error to a single file is

Code:

Sun Dec 21 03:59:14 SGT 2014 > test5.sh > output.txt 2>&1

Q1) How is a command being interpreted in linux , the sequence in which it is interpreted ? from left to right ? right to left ?

Shouldn't it be

Code:

test5.sh 2>&1 1>output.txt 
or 
test5.sh 2>&1>output.txt ?

Regards,
Noob