Questions tagged [pattern-matching]
The pattern-matching tag has no usage guidance.
0
votes
4answers
42 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
31 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
62 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
41 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
35 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
50 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
12 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....
1
vote
2answers
161 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
252 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
181 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
56 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
38 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
127 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
55 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
59 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
100 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
...
3
votes
2answers
400 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
795 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
55 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?
...
