In my script shell, i have 2 files. The first one is a file containing only names of files with part of the path :
list1:
aaa/bbb/file1.ext
ccc/ddd/file2.ext
eee/fff/file3.ext
The second one is a list of every files of the extension ".ext" with the absolute path before them:
list2:
/home/.../aaa/bbb/file1.ext
...
...
...
/home/...ccc/ddd/file2.ext
...
And I am trying to extract the lines of the second file list2, containing the lines of the first one with grep.
For now I tried :
while read line
do
grep "$line" "list1"
done < list2
But this command doesn't ouptut anything, however the command
grep "aaa/bbb/file1.ext" "list1"
have the output I am waiting for
/home/.../aaa/bbb/file1.ext
Anyone sees what I am missing on this script? Thanks
This is one of the cases where -f option from grep comes very handy:
grep -f f1 f2
For your given input returns:
/home/.../aaa/bbb/file1.ext
/home/...ccc/ddd/file2.ext
From man grep:
-f FILE, --file=FILE
Obtain patterns from FILE, one per line. The empty file contains zero
patterns, and therefore matches nothing. (-f is specified by
POSIX.)
Related
Tried the following command, it lists all the lines including file names
which are not matching the given pattern.
grep -nrv "^type.* = .*"
"But what we need is list of file names in a folder with content
which does not have even a single occurrence of above pattern."
Your help will be really appreciated.
You need the -L option:
grep -rL '^type.* = .*' directory_name
From the GNU grep manual:
-L, - -files-without-match
Suppress normal output; instead print the name of each input file from which no output would normally have been printed. The scanning will stop on the first match.
I have a text file chunk_names.txt that looks like this:
chr1_12334_64321
chr1_134435_77474
chr10_463252_74754
chr10_54265_423435
chr13_5464565_547644567
This is an example but all chromosomes are represented (1...22, X and Y). All entries follow the same formatchr{1..22, X or Y}_*string of numbers*__*string of numbers*.
I would like to split these into per chromosome files e.g. all of the chunks starting chr10 to be put into a file called chr10.txt:
In Linux I have tried :
for i in {1..22}
do
grep chr$i chunk_names.txt > chr$i.txt
done
However, the chr1.txt output file now contains all the chromosome chunks with 1 in them (1,10,11,12, etc).
How would I modify this script to separate out the chromosomes?
I also haven't tackled how to include chromosome X or Y within the same script and am currently running that separately
Things I have tried :
grep -o gives me just "chr$i" as an output
grep 'chr$i' gives me blank files
grep "chr$i" has the initial problem
Many thanks for your time.
Your 'for' loop will mean parsing your file N times (where N is the number of chromosomes/contigs in your list). Here's an agnostic approach using awk that will parse the file just once:
awk -F '_' '{ print > $1 ".txt" }' chunk_names.txt
If you include the _ following the number you can distinguish between chr1_ and e.g. chr10_. To include X and Y, simply include these in the loop
for i in {1..22} X Y
do
grep "chr${i}_" chunk_names.txt > chr$i.txt
done
To search at the beginning of the line only you can add a leading ^ to the pattern
grep "^chr${i}_" chunk_names.txt > chr$i.txt
Explanation about your attempts:
grep chr$i searches for the pattern anywhere in the line. The shell replaces $i with the value of the variable i, so you get chr1, chr2 etc.
If you enclose the pattern in double quotes as grep "chr$i" the shell will not do any file name globbing or splitting of the string, but still expand variables. In your case it is the same as without quotes.
If you use single quotes, the shell takes the literal string as is, so you always search for a line that contains chr$i (instead of chr1 etc.) which does not occur in your file.
Explanation about quotes:
The quotes in my proposed solution are not necessary in your case, but it is a good habit to quote everything. If your pattern would contain spaces or characters that are special to the shell, the quoting will make a difference.
Example:
If your file would contain a chr1* instead of the chr1_, the pattern chr${i}* would be replaced by the list of matching files.
When you already created your output files chr1.txt etc., try these commands
$ i=1; echo chr$i*
chr10.txt chr11.txt chr12.txt chr13.txt chr14.txt chr15.txt chr16.txt chr17.txt chr18.txt chr19.txt chr1.txt
$ i=1; echo "chr$i*"
chr1*
In the first case, the grepcommand
grep chr${i}* chunk_names.txt
would be expanded as
grep chr10.txt chr11.txt chr12.txt chr13.txt chr14.txt chr15.txt chr16.txt chr17.txt chr18.txt chr19.txt chr1.txt chunk_names.txt
which would search for the pattern chr10.txt in files chr11.txt ... chr1.txt and chunk_names.txt.
I have searched extensively on the internet about this but haven't found much details.
Problem Description:
I am using aix server.
I have a pattern.txt file that contains customer_id for 100 customers in the following sample format:
160471231
765082023
75635713
797649756
8011688321
803056646
I have a directory (/home/aswin/temp) with several files (1.txt, 2.txt, 3.txt and so on) which are pipe(|) delimited. Sample format:
797649756|1001|123270361|797649756|O|2017-09-04 23:59:59|10|123769473
803056646|1001|123345418|1237330|O|1999-02-13 00:00:00|4|1235092
64600123|1001|123885297|1239127|O|2001-08-19 00:00:00|10|1233872
75635713|1001|123644701|75635713|C|2006-11-30 00:00:00|11|12355753
424346821|1001|123471924|12329388|O|1988-05-04 00:00:00|15|123351096
427253285|1001|123179704|12358099|C|2012-05-10 18:00:00|7|12352893
What I need to do search all the strings from pattern.txt file in all files in the directory, in first column of each file and list each filename with number of matches. so if same row has more than 1 match it should be counted as 1.
So the output should be something like (only the matches in first column should count):
1.txt:4
2.txt:3
3.txt:2
4.txt:5
What I have done till now:
cd /home/aswin/temp
grep -srcFf ./pattern.txt * /dev/null >> logfile.txt
This is giving the output in the desired format, but it searching the strings in all columns and not just first column. So the output count is much more than expected.
Please help.
If you want to do that with grep, you must change the pattern.
With your command, you search for pattern in /dev/null and the output is /dev/null:0
I think you want 2>/dev/null but this is not needed because you tell -s to grep.
Your pattern file is in the same directory so grep search in it and output pattern.txt:6
All your files are in the same directory so the -r is not needed.
You put the logfile in the same directory, so the second time you run the command grep search in it and output logfile.txt:0
If you can modify the pattern file, you write each line like ^765082023|
and you rename this file without .txt
So this command give you what you look for.
grep -scf pattern *.txt >>logfile
If you can't modify the pattern file, you can use awk.
awk -F'|' '
NR==FNR{a[$0];next}
FILENAME=="pattern.txt"{next}
$1 in a {b[FILENAME]++}
END{for(i in b){print i,":",b[i]}}
' pattern.txt *.txt >>logfile.txt
I want to know What is the difference between the two command:
ls l file; grep *pl file
ls l file; grep ".*pl" file
First off - ";" is a command separator on shell. So the above will execute two different commands sequentially.
So that makes there are three different commands:
$ ls l file
This command will try to list two files namely "l" and "file". It will display the file names if they exist or error out if they do not.
$ grep *pl file
This is trickier. It will try to first replace * with the contents of the current directory. Whichever way it expands, it will append pl to it and try to grep that entire shell expanded pattern in the file. The output entirely depends upon the contents of your current directory.
$ grep ".*pl" file
This will do a greedy match of the pattern ".*pl" in the file. That means it will match all lines in the file which has a pattern: followed by "pl"
Try this yourself and you would understand what's happening.
I am performing a recursive fgrep/grep -f search on a zipped up folder using the following command in one of my programs:
The command I am using:
grep -r -i -z -I -f /path/to/pattern/file /home/folder/TestZipFolder.zip
Inside the pattern file is the string "Dog" that I am trying to search for.
In the zipped up folder there are a number of text files containing the string "Dog".
The grep -f command successfully finds the text files containing the string "Dog" in 3 files inside the zipped up folder, but it prints the output all on one line and some strange characters appear at the end i.e PK (as shown below). And when I try and print the output to a file in my program other characters appear on the end such as ^B^T^#
Output from the grep -f command:
TestZipFolder/test.txtThis is a file containing the string DogPKtest1.txtDog, is found again in this file.PKTestZipFolder/another.txtDog is written in this file.PK
How would I get each of the files where the string "Dog" has been found to print on a new line so they are not all grouped together on one line like they are now?
Also where are the "PK" and other strange characters appearing from in the output and how do i prevent them from appearing?
Desired output
TestZipFolder/test.txt:This is a file containing the string Dog
TestZipFolder/test1.txt:Dog, is found again in this file
TestZipFolder/another.txt:Dog is written in this file
Something along these lines, whereby the user is able to see where the string can be found in the file (you actually get the output in this format if you run the grep command on a file that is not a zip file).
If you need a multiline output, better use zipgrep :
zipgrep -s "pattern" TestZipFolder.zip
the -s is to suppress error messages(optional). This command will print every matched lines along with the file name. If you want to remove the duplicate names, when more than one match is in a file, some other processing must be done using loops/grep or awk or sed.
Actually, zipgrep is a combination egrep and unzip. And its usage is as follows :
zipgrep [egrep_options] pattern file[.zip] [file(s) ...] [-x xfile(s) ...]
so you can pass any egrep options to it.