Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to extract the partial matching strings among two files? Post 303035964 by RudiC on Tuesday 11th of June 2019 03:29:16 AM
Old 06-11-2019
No surprise "it is not working" as none of your attempts is addressing your problem if at all syntactically correct.



Code:
awk 'FNR == NR {SRCH[$3 "-" $2]; next} $2 in SRCH {print ">" $0}' FS="[]- []*" file1 RS=">" ORS="" FS="[:
]" file2 
>Contig_152:50833-51615
CGGAGTAGCTTCGATCAGCGTGACCGGTACCGAGCGACCGTCTTCAGTGAAGACGCGGCT
CATACCAGCCTTGCGGCCCACGAAGCCCAACGAATATTTCTTCGTCATGGTCGTAGTCCT
CAGGTCAGCTTGATCTGGACGTCGACGCCAGCCGCGAGTTCGAGCTTCATCAGCGCGTCC
ACGGTCTTGTCGTTCGGGTCGACGATATCGAGCACACGCTTGTGCGTGCGGGTTTCGTAT
TGG
>Contig_152:50215-50829
TGCCAGCCACTCCTCGACCTTCTTGACCGCGTCGGCGGTGATCACGACCGTATCGGCCCC
GACCAGAGCGACCGGATCCAGACCCTGCACGTCACGCACCTGCACATACGGCAGGTTGCG
AGCGGACAGATACAGGTGCTCGGAAGCCTCTTCGGTGACGATCAGCGGGCGCTTGCCCAC
>Contig_152:45550-46116
GTTACGGAACGGGAACTTGAACGCTGCCAGCAGCGCCTTCGCTTCCGCATCCGTCTTGGC
GGTGGTGGTGATGGCGATATCCATACCGCGGATCGCGTCGACGGCGTCGAAGTCGATTTC
>Contig_152:44079-44618
AGCCTTCTTGGCTTCCTTGCGAATGATGACTTCACCGGCGTACTTCACACCCTTGCCCTT
GTAGGGCTCCGGCGGACGGAAACCGCGAATCTTGGCGGCAACTTCGCCGACGCGCTGCTT

Your desired output for "45550-46116" is missing a trailing "C".

Last edited by RudiC; 06-13-2019 at 05:02 AM..
These 2 Users Gave Thanks to RudiC For This Post:
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Grep all files matching partial filename

What would be the easiest way to grep all files within a particular directory that match a partial filename? For example, searching all files that begin with "filename.txt" and are appended with the date they were created. I am using Ksh 88, btw. (3 Replies)
Discussion started by: mharley
3 Replies

2. Shell Programming and Scripting

is it hard to extract particular lines & strings from the files??

Hi Experts, I have lots of big size files. Below is the snapshot of a file. From the files i want extract informmation like belows. What could be command or script for that? DELETE RESP:940120105 CREATE RESP:0 GET RESP:0 File contains like below- ... ... <log... (8 Replies)
Discussion started by: thepurple
8 Replies

3. Shell Programming and Scripting

awk/sed to extract column bases on partial match

Hi I have a log file which has outputs like the one below conn=24,196 op=1 RESULT err=0 tag=0 nentries=9 etime=3,712 dbtime=0 mem=486,183,328/2,147,483,648 Now most of the time I am only interested in the time ( the first column) and a column that begins with etime i.e... (8 Replies)
Discussion started by: pkabali
8 Replies

4. Shell Programming and Scripting

Extract partial string from path.

Hi all, i've a string $DIR=/u/user/NDE/TEST_LOGS/20110622_000005_TEST_11_HD_120/HD/TEST_11_HD_120/hd-12 i need to extract string from 2011.... i.e i need it as 20110622_000005_TEST_11_HD_120 as matched string, and in turn i need to split values 20110622_000005_TEST_11_HD_120 into two.... (6 Replies)
Discussion started by: asak
6 Replies

5. Shell Programming and Scripting

matching strings from different files

I want to compare file 1 to file 2 and if a string from file 1 appears in file 2, then print the file 2 row, where the string appears, onto file3. file 1 looks like this. DOG_0004340 blah blah2 j 22424 DOG_3010311 blah blah3 o 24500 DOG_9949221 blah blah6 x 35035 file 2 looks like... (5 Replies)
Discussion started by: verse123
5 Replies

6. UNIX for Dummies Questions & Answers

Extract columns by matching ids in two files

Hello, I want to extract columns from file2 to file3 by matching ids between file1 and file2. The extracted columns should be in same order as file1 ids. for example: file1.txt 1823 607 R2A9 802 771 file2.txt 1823 1 2 4 22 11 4 29 607 12 3 3 R2A9... (8 Replies)
Discussion started by: ryan9011
8 Replies

7. Shell Programming and Scripting

Concatenating 2 lines from 2 files having matching strings

Hello All Unix Users, I am still new to Unix, however I am eager to learn it.. I have 2 files, some lines have some matching substrings, I would like to concatenate these lines into one lines, leaving other untouched. Here below is an example for that.. File 1 (fasta file): >292183... (6 Replies)
Discussion started by: Mohamed EL Hadi
6 Replies

8. Shell Programming and Scripting

awk extract strings matching multiple patterns

Hi, I wasn't quite sure how to title this one! Here goes: I have some already partially parsed log files, which I now need to extract info from. Because of the way they are originally and the fact they have been partially processed already, I can't make any assumptions on the number of... (8 Replies)
Discussion started by: chrissycc
8 Replies

9. Shell Programming and Scripting

URL partial matching

I have two files: file 1 http://www.hello.com http://neo.com/peace/development.html, www.japan.com, http://example.com/abc/abc.html http://news.net http://lolz.com/country/list.html,www.telecom.net, www.highlands.net, www.software.com http://example2.com ... (1 Reply)
Discussion started by: csim_mohan
1 Replies

10. UNIX for Beginners Questions & Answers

Match patterns between two files and extract certain range of strings

Hi, I need help to match patterns from between two different files and extract region of strings. inputfile1.fa >l-WR24-1:1 GCCGGCGTCGCGGTTGCTCGCGCTCTGGGCGCTGGCGGCTGTGGCTCTACCCGGCTCCGG GGCGGAGGGCGACGGCGGGTGGTGAGCGGCCCGGGAGGGGCCGGGCGGTGGGGTCACGTG... (4 Replies)
Discussion started by: bunny_merah19
4 Replies
comm(1) 							   User Commands							   comm(1)

NAME
comm - select or reject lines common to two files SYNOPSIS
comm [-123] file1 file2 DESCRIPTION
The comm utility reads file1 and file2, which must be ordered in the current collating sequence, and produces three text columns as output: lines only in file1; lines only in file2; and lines in both files. If the input files were ordered according to the collating sequence of the current locale, the lines written will be in the collating sequence of the original lines. If not, the results are unspecified. OPTIONS
The following options are supported: -1 Suppresses the output column of lines unique to file1. -2 Suppresses the output column of lines unique to file2. -3 Suppresses the output column of lines duplicated in file1 and file2. OPERANDS
The following operands are supported: file1 A path name of the first file to be compared. If file1 is -, the standard input is used. file2 A path name of the second file to be compared. If file2 is -, the standard input is used. USAGE
See largefile(5) for the description of the behavior of comm when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes). EXAMPLES
Example 1 Printing a list of utilities specified by files If file1, file2, and file3 each contain a sorted list of utilities, the command example% comm -23 file1 file2 | comm -23 - file3 prints a list of utilities in file1 not specified by either of the other files. The entry: example% comm -12 file1 file2 | comm -12 - file3 prints a list of utilities specified by all three files. And the entry: example% comm -12 file2 file3 | comm -23 -file1 prints a list of utilities specified by both file2 and file3, but not specified in file1. ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of comm: LANG, LC_ALL, LC_COLLATE, LC_CTYPE, LC_MESSAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 All input files were successfully output as specified. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |enabled | +-----------------------------+-----------------------------+ |Interface Stability |Standard | +-----------------------------+-----------------------------+ SEE ALSO
cmp(1), diff(1), sort(1), uniq(1), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.11 3 Mar 2004 comm(1)
All times are GMT -4. The time now is 10:09 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy