Search 2 Strings Using Awk

Hi all ,
I have a requirement where I have a file. Contents of the file are :
#comments
VAR="abg"
RES=123
#comments
IC6790ABG="https://www.abc.com"
IC5678-vg="https://www.bhy.com"
IC-gy_567:78="https://www.gyt.com"
#comments
The variable names can not have characters like - , : so
in this file I have to find words starting with IC and replace characters like - ,:
I want to change only the variable name , not the whole line.
I have used SED command

sed -i '/^IC/s/[^0-9 a-z A-Z _]*//g' file

when I am using this command , it is replacing the whole line
output becomes :

#comments
VAR="abg"
RES=123
#comments
IC6790ABGhttpswwwabccom
IC5678vghttpswwwbhycom
ICgy56778httpswwwgytcom
#comments


But I want the output like this :

#comments
VAR="abg"
RES=123
#comments
IC6790ABG="https://www.abc.com"
IC5678vg="https://www.bhy.com"
ICgy_56778="https://www.gyt.com"
#comments

How can I get the desired output , thanks for your help in advance .

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 have the following code to extract two dates using awk, which are then read into two awk variables new and old respectively.
Each dates on the html file pulled with curl request is in this format:
2015-04-06 09:40:37
And two are being extracted
However the strings are being split on white space within the date strings. I tried changing OFS to ',', but it was still splitting incorrectly.
Code:

read dateStrNew dateStrOld < <(curl -k -q "$curl_call" | html2text | gawk '/Newest Sequence/ { new=$3" "$4 }/Oldest Sequence/ \
 {old=$3" "$4}END {OFS=","; print new,old }')  //new = date, old = date

Both parts of the date are being assigned to each variable using $3 and $4, then the space needs to be added back in so that the string can be used afterwards with a date command.

I just can't work out what is wrong, any help would be very much appreciated! Thanks!

I am using the following two commands to output CPU and RAM usage on a Linux machine.

Code:

/bin/grep 'cpu ' /proc/stat | awk '{usage=($2+$4)*100/($2+$4+$5)} END {print usage "%"}'

/usr/bin/free | grep Mem | awk '{print $3/$2 * 100.0 "%"}'

My problem is that the output is like this

Quote:
5.33672%
13.9723%
Is there a way to output a single number? For example

Quote:
5
13
Thank you

Hi guys,

I have multiple .csv files with multiple columns/headings, set up essentially like this (obviously more info in the real thing)


Gene Location Ref Var Coverage Function
DMD chrX.... A G 198 exonic
SCN4A chr17.... T C 111 splicing

and so on...

How could I concatenate selected columns into an output file with strings seperated with a comma? eg DMD,A,G,exonic (similar to what you can do in excel). I would like to be able to do this for multiple files in a directory. It would be preferable if all the outputs could be compiled into one file as I'll use this for something else later.
The current protocol in our team is to concatenate each file individually with an excel macro and copy into a file, and it takes a very long time.

Thanks very much!!

I've been using this a lot:

find <directory to start search at> -name "<files to search in>" -type f | xargs grep "<string to search for>"

e.g.

find /usr/include -name "*.h" -type f | xargs grep "#define UINT"

now what if I wanted to output the results to a file?

Hello

I have a text file which has blocks like
Code:

dir1/dir2/dir3/name_run_number1:
line1_run_number1_part1
line2_run_number1_part2
line3_run_number1_part3...

Each block is separated with a blank line and there is the ":" in the "header" of each one while each block carries the same "number1" after "run_" suffix
What I want to do is for each block, extract the "number1" as shown in the first line and then for the lines below count from 1-20 and give a message if a "partX" line is missing. Any bash or python would be fine

Thanks

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

How can I get shell to read special characters as strings? Such as $ or !

Code:

$ ./test.sh "!hooray!"
bash: !hooray!: event not found
$ ./test.sh !hooray!
bash: !hooray!: event not found

If I escape it, the \ prints in the output:
Code:

$ ./test.sh "\!hooray\!"
\!hooray\!

The code of test.sh is as follows:
Code:

$ cat test.sh 
#!/bin/bash
str="$1"
echo "$str"

TIA

Hi,

Below is the output of the "date" command:
Thu Apr 2 16:07:59 SGT 2015

After assigning the output to a parameter as follows:
DATE=`date`

The output has changed when "echo $DATE":
Thu Apr 2 16:09:40 SGT 2015
^^

The "2" has moved forward.

I don't want the "2" to move forward, please advise how to go about it.

Thanks in advance.