Questions tagged [pattern-matching]
The pattern-matching tag has no usage guidance.
43
questions
0
votes
1answer
62 views
Zsh string pattern match to delete spaces
Trying to solve a code-golf problem using zsh, but my regex isn't working correctly.
Requirement Given input string $1, delete all spaces immediately to the left of any ! character.
Examples:
...
0
votes
1answer
21 views
Segregate results from a file using awk or sed after matching multiple patterns
From one of our application logs that contains a bunch of INFO messages, and system out lines, I want to be able to extract lines that are contained within 2 patterns and then specifically get values ...
0
votes
1answer
27 views
'expect' not matching server response string
I'm using a bash script to log into a telnet server and execute a number of commands. It looks like:
login_and_run.sh
#!/bin/bash
unset TELNET_USER_NAME_STRING
unset TELNET_PASSWORD_STRING
unset ...
2
votes
3answers
62 views
How to find the last occurrence of a string in column 1 and replace the corresponding value in column 3?
I have three columns in a file as such:
apple1 10109283 20012983
apple1 10983102 10293809
apple1 10293893 2349823049
apple10 109283019 109238901
apple10 ...
0
votes
2answers
41 views
Extract match and everything before next match, do it for every match
I have a file with this structure:
>Cluster 0
0 51aa, >MG00HS05:520:C8M1TACXX:3:1101:1428:2080/1... *
1 51aa, >MG00HS05:520:C8M1TACXX:3:1101:1658:2480/1... at 3:51:1:49/96.08%
2 ...
0
votes
0answers
28 views
grep -f not working with file
I have a file with having patterns separated by new line characters.
which matches the patterns i want to find from a file.
but when i run command
grep -f patterns_file words_file
It gives no ...
0
votes
3answers
112 views
Checking whether a word (value) is in a comma-separated list
In below code, 2 should not match with 21,
but it gives a result "matched".
How can I check whether the SOURCE value is in the LIST?
LIST="1,21,3,4"
SOURCE="2"
if echo "$LIST" | grep -q "$SOURCE"; ...
1
vote
2answers
33 views
sed or awk to print between 2 patterns[excluding the patterns] [duplicate]
I have the following text..
[start]
this
is my line
[end]
My output should be:
this
is my line
Need help..
Tried a combination of :
sed -n '/start/,/end/p' $File & sed -e "s/]/']/" -e "s/\[/...
1
vote
1answer
42 views
Odd behavior (bug?) of sed when using $
I've got a problem and I am not sure whether this is a bug or if this is supposed to happen when using $ for addressing lines. Basically, I have the following command:
sed -e '$s/test/tset/g'
...
0
votes
2answers
37 views
How to grep a string with any two numbers that match or that have the first number one less than the second number?
I have a tab delimited file with four columns. I would like to grep for the lines that have a specific pattern in column 1, where it says apple M of N.
I only want to extract the lines that have the ...
0
votes
1answer
35 views
Extract pattern in perl
Is it possible to have just one regex which can extract the pattern "Mango-1.whatever.." in any of these 3 conditions (i.e. $dummy). I keep printing everything after this pattern. If I use comma in ...
2
votes
1answer
54 views
How do I avoid greping matching lines with -
I'm trying to grab only matching lines from a file using grep. The problem is that, when for example I use the following expression:
grep -w AFFX-KIT-000088 textfile
it will return:
AFFX-KIT-000088-...
6
votes
4answers
736 views
Write a function that checks if a string starts with or contains something
I want to write a function that checks if a given variable, say, var, starts with any of the words in a given list of strings. This list won't change.
To instantiate, let's pretend that I want to ...
0
votes
2answers
63 views
AWK Split Variable
I have the following sequence in a file:
AA
MUi
MUi-j
MUi-N
ABk
ABk-l
ABk-N
MBk(i)
MBk-l(i)
MBk-l(i-j)
MBk-l(i-N)
MBk-N(i-j)
MBk-N(i-N)
I want to split it in small pieces:
The first two chars will ...
3
votes
0answers
27 views
Should I set the locale to `C` when matching a range of numbers?
If I wanted to search for lines in a file that contain a or b or c or d I would run
LC_COLLATE=C grep -E '[a-d]' file_to_search
or
LC_ALL=C grep -E '[a-d]' file_to_search
If I fail to set the ...
2
votes
0answers
24 views
why does recursive searching with grep print fewer lines when using \bSTRING\b compared to the -w option?
There are two ways to read all files under the current working directory:
grep -rw pip | wc -l
grep -r "\bpip\b" | wc -l
Assuming 1 and 2 both search the working directory for the whole word "pip", ...
28
votes
2answers
1k views
What is the difference between `a[bc]d` (brackets) and `a{b,c}d` (braces)?
What is the difference between a[bc]d and a{b,c}d? Why do people use a{b,c}d when there is already a[bc]d?
0
votes
0answers
17 views
Find longest matching portion (not in the same offset) within two files
I am wondering if I can compare two files and find longest matching portion not in the same offset
Example:
File1: 0022222100022222
File2: 0333310003333333
I need to find the matching value (1000) ...
0
votes
2answers
48 views
Extracting lines to new files
Say I have a large CSV file with a header and several columns. For the purpose of this question I will consider a small file with just two columns. We can call it use_rep.
user_id,rep
885,500K+
22565,...
0
votes
1answer
183 views
Log the files found with the linux find and sed command
I have a folder with txt, html, jpg and png files.
Now I want to go over all textbased files (txt and html) and start a search and replace.
I did the following and it is working fine:
find ./ -...
1
vote
1answer
48 views
Compare two text files, extract matching rows of file2 plus additional rows
have been mocking around with this too long and tried grep, join, awk but I cant get the parameters right. I need to get the command right.
I have got two text files.
cat file1
@ABC:11:ABC:1:...
2
votes
1answer
40 views
WildCard Find Replace CP
I'm trying to replace files that match a particular pattern* on CentOS, but it is not working.
I initially wrote:
cp example.com/(*)/orm-mysql/build/conf/(*)-conf.live.php example_dev.com/$1/orm-...
2
votes
4answers
586 views
Parse all strings of specific length?
I've exported my email archive of 10 years which is very large.
I want to parse all the text for any string that is 64 characters long in search of a bitcoin private key.
How can I parse strings of ...
0
votes
4answers
53 views
How to extract word which has only numbers separated by 'dot'
From below lines
abcd efgh ijhk lmn opqrs 9.0.8.2c tuv wxyz
abcd efgh ijhk lmn opqrs 8.1.3.9b
How to extract only
9.0.8.2c
8.1.3.9b
0
votes
1answer
240 views
Sed search and delete matching two patterns one of which is a variable
I have a file that contains multiple instances of code that I need to delete. Here is an example:
!/bin/bash
mkdir /rootdir/pipeline_runs/oncology/analysis/sample_1_NA172_1
cd /rootdir/pipeline_runs/...
-3
votes
1answer
130 views
Extract data between two patterns from a huge (forced) text file
I have filename.json. If I parse it in terminal with
file filename.json
output is:
filename.json: UTF-8 Unicode text, with very long lines
wc -l filename.json
1 filename.json
If I parse it ...
1
vote
2answers
615 views
grep contents of one list with another
I have 2 files and I want to grep on them
List1
ACY1
RPL3
RPL4
List2
1 ABHD14A-ACY1
2 ACY1
3 RPL34
4 RPL21
5 RPL3
6 RPL41
I tried something like this
grep -Fwf list1.txt list2.txt ...
0
votes
1answer
467 views
How to negate Bash's Regular Expression Matching Operator
Bash has the =~ regular expression matching operator. Here is an example of using it:
#!/bin/bash
input=$1
if [[ "$input" =~ "[0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9][0-9][0-9]" ]]
# ^ ...
-2
votes
2answers
82 views
Find longest stretch of pattern from centre of sequence
How to calculate the longest consecutive pattern of C/T anywhere in sequence and longest consecutive pattern of C/T from centre
CCCCTGTTGCCAAACAATGC
TTTTCCCGCCTTTGGCCTAC
...
0
votes
1answer
15 views
how to match a column of a file 1 to text of another file 2 then if it matches print file 2
File 1
Name,TaxID,Lineage,Count,Proportion_All(%),Proportion_Classified(%)
Acaryochloris marina,155978,Bacteria;Cyanobacteria;;Synechococcales;Acaryochloridaceae;Acaryochloris,4,0.000218669,0....
2
votes
2answers
744 views
Use sed to print selected lines within a range
Consider the simplified file
AAA
BBB
CCC1
DDD
EEE
CCC2
DDD
FFF
GGG
CCC3
HHH
I can pick out the range EEE to FFF with
sed -n '/EEE/,/FFF/p'
Suppose though that I want to print any line containing C ...
4
votes
5answers
268 views
Count the longest stretch of consecutive patterns
I have a sequence file:
$ cat file
CACCGTTGCCAAACAATG
TTAGAAGCCTGTCAGCCT
CATTGCTCTCAGACCCAC
GATGTACGTCACATTAGA
ACACGGAATCTGCTTTTT
CAGAATTCCCAAAGATGG
I want to calculate the longest stretch of C+T. I ...
0
votes
2answers
484 views
grep multiple patterns with different context
I have a file roughly like
header_one
param1
param2
...
data_one
data1
data2
data3
data4
...
header_two
param1
param2
...
data_two
data1
data2
data3
data4
I'd like to extract all header blocks ...
0
votes
2answers
108 views
Pattern recognition betweel two sentences in a file which has spaces and special characters?
I have a file in which I want to print all the lines between two patterns. Pattern1 = # Begin TRACE A Data and Pattern 2 =# Done Data $capture, I want to print every line between pattern1 and pattern2....
0
votes
1answer
43 views
For a given string(2 or 3 word) in a .txt file and print the whole line. [duplicate]
My .txt file contains these kind of content :
The Law and Lawyers of Pickwick, by Frank Lockwood 21214
Frankenstein, by Mary Wollstonecraft 20
The first ...
0
votes
1answer
263 views
print out lines if first three columns match the first three columns in another file
I have file1 which has 3 columns and file2 which has 8 columns. What I wanted to do was if the first 3 columns in file 2 were found in file 1, then print out the entire 8 columns in file 2.
I have ...
0
votes
1answer
143 views
Pattern recognition and summing columns between two csv/excel files
I have two files, in which one has data on each person's start date, increment, promotion and other details, and the other file has their research output over the years. Can a script be written in ...
1
vote
1answer
72 views
Match lines between two patters using sed just once [duplicate]
Given: sed -e '/pattern1/,/pattern2/!d' file.org
How can I match the first occurrence of the lines between pattern1 and pattern2, but not the rest?
For example:
pattern1
aaaa
pattern2
pattern1
bbb
...
3
votes
3answers
218 views
Comparing two files linewise and if pattern of file 1 is not found (fully or partially) in file 2 then print line of file 1
I have two files:
file1 (search):
1
GACGGAGGATGCAAGTGTTATCCGGAATCACTGGGCGTAAAGTTTTTTTTT
2
GACGGAGGATGCAAGTGTTATCCGGAAT
3
GACGGAGGATGCAAGTGTTATCCGGAATCACTGGGCGTAAAGCGTCC
4
...
5
votes
1answer
1k views
How to grep MATCH colored input?
Say I have output from a command that is colorized for the terminal. I want to match any line that contains the color yellow. How can I do this in grep, eg: mycommand -...
0
votes
3answers
4k views
Grep for word stem and print only word (and not line)
I'm trying to print only a matching word that are found through a regular expression. Below, I want all the OPENSSL_NO_* options that are present in the source code:
$ grep -IR OPENSSL_NO
fuzz/asn1.c:...
0
votes
0answers
58 views
grep a sequnce of 'AB<anything>CDE' [duplicate]
I want to grep for 'AB...CDE', where ... stands for anythings until CDE first occurs.
I have tried grep 'AB*CDE' filename but this matches til the last occurrence of CDE.
How can fix this?
...
7
votes
1answer
738 views
Is there a Unix command that searches for similar strings, based mostly on how they sound when spoken?
I have a file of names, and I want to search within it, not caring too much about whether I have spelled the name ( that I am searching for ) correctly. I know that grep has quite a bit of ...
