Problem using variable as pattern in grep

[johnsmithgr8]

Hi all,

I am working as computational chemist and regularly use bash scripting to simplify my work. I have been using grep command successfully to extract data from log files of different softwares. However, today i came across a weired problem working with grep

Here is what i am trying to do
1. store the path to a file1 in variable "file1"
2. get basename of file2
3. match basename of file2 with an integer (in file3) and save it in another variable "x"
4. get the line containing "x" from file1

Following code does not work and there is no output from the last grep command

file1="/path/to/file"
bname=`basename ${file2} .csv
x=`grep -w "${bname}" file3 | awk -F "," '{print $3"}'`
grep -w "${x}" ${file1}

I would like to mention the if i manually save the integer value in variable "x", then the last command works

x=532540
grep -w "${x}" ${file1}

output:532540,104.45,342391442.00,

Please suggest me where i am going wrong. any help in this matter will be of great importance to me.

Thanking you all in advance

[markcole]

Hi all,

I am working as computational chemist and regularly use bash scripting to simplify my work. I have been using grep command successfully to extract data from log files of different softwares. However, today i came across a weired problem working with grep

Here is what i am trying to do
1. store the path to a file1 in variable "file1"
2. get basename of file2
3. match basename of file2 with an integer (in file3) and save it in another variable "x"
4. get the line containing "x" from file1

Following code does not work and there is no output from the last grep command

file1="/path/to/file"
bname=`basename ${file2} .csv
x=`grep -w "${bname}" file3 | awk -F "," '{print $3"}'`
grep -w "${x}" ${file1}

I would like to mention the if i manually save the integer value in variable "x", then the last command works

x=532540
grep -w "${x}" ${file1}

output:532540,104.45,342391442.00,

Please suggest me where i am going wrong. any help in this matter will be of great importance to me.

Thanking you all in advance

Without knowing the content of the files to test, adn assuming that what you have typed in the code section is exactly what you are trying to do, I would say you have an extra quote after the $3 in the awk statement. Other than that, it looks fine.

file1="/path/to/file"
bname=`basename ${file2} .csv
x=`grep -w "${bname}" file3 | awk -F "," '{print $3}'`
grep -w "${x}" ${file1}

[Manko10]

There are some syntax errors in the skript. I would also suggest using the parenthesis operator instead of backticks for command substitution. See if that works:

file1="/path/to/file"
bname=`basename ${file2} .csv`
x=$(grep -w "${bname}" file3 | awk -F "," '{print "$3"}')
grep -w "${x}" ${file1}

To give you further advice we need to know the contents of your file.

[johnsmithgr8]

Dear all,

thank you very much for your suggestions and pointing out the mistake in code.
however, after making the corrections also, it was not working

finally trying to find some workaround, i came to know that it was file3 which was the source of problem. Since content of the file3 are not going to be modified, i exchanged column2 (string) with column3 (integer)., and then tried the following

file1="/path/to/file"
bname=`basename ${file2} .csv
x=`grep -w "${bname}" file3 | awk -F "," '{print $2}'`
grep -w "${x}" ${file1}

in the above case, variable "x" contains integer value, and it works.

however, minor modification of the above code (required in another script) extracts the data contained in column 3 (string) of the file3.

file1="/path/to/file"
bname=`basename ${file2} .csv
y=`grep -w "${bname}" file3 | awk -F "," '{print $3}'`
echo "y:$y"

expected output: y:hartree
output: y:hartree?

in this case, variable "y" contains the expected string value, but it is always appended by a question mark (?).

I guess, the problem was may be with end line character. so I added a fourth column in file3 containing all integer zero values. then both the above code works fine. Although, i have the code working, i would like to know the reason for such behavior, so that i can take care of it in future.

Once again than you for your support and suggestions

john

[dufftime]

Windows EOL? You can use "cat -A file" to show hidden characters and EOL stuff. I got bit by Windows EOL just yesterday.