Sponsored Content
Top Forums UNIX for Dummies Questions & Answers print multiple lines from text file based on pattern list Post 302555416 by Oyster on Wednesday 14th of September 2011 04:41:04 PM
Old 09-14-2011
print multiple lines from text file based on pattern list

I have a text file with a list of items/patterns:

ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig12238
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig34624
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig56875
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig70306
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig71435
...

I would like to print those lines which match from a tab-delimited file containing many many more lines:

...
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60558 1086
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60559 641 95 14.038 ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60559 731
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60560 620 1406 245.247 ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60560 625
ConsensusfromCGX_alldays_trimmedcollapsedfilteredreadscontiglist(229095contigs)contig60561 609 208 36.771
...

Can grep process a pattern file? It seems as if it should, however, I have not had success. sed, awk? Please help. Thanks.
 

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Merge lines in text file based on pattern

Hello, I have searched forum trying to find a solution to my problem, but could not find anything or I did not understand the examples.... I should say, I am very inexperienced with text processing. I have a text file with approx 60k lines in it. I need to merge lines based on the number... (8 Replies)
Discussion started by: Bertik
8 Replies

2. Shell Programming and Scripting

Awk: print lines with one of multiple pattern in the same field (column)

Hi all, I am new to using awk and am quickly discovering what a powerful pattern-recognition tool it is. However, I have what seems like a fairly basic task that I just can't figure out how to perform in one line. I want awk to find and print all the lines in which one of multiple patterns (e.g.... (8 Replies)
Discussion started by: elgo4
8 Replies

3. Shell Programming and Scripting

Split a text file into multiple pages based on pattern

Hi, I have a text file (attached the sample). I have also, attached the way the way the files need to be split. We get this file, that will either have 24 Jurisdictions, or will miss some and retain some. Like in the attached sample file, there are only Jurisdictions 03,11,14,15, 20 and 30.... (3 Replies)
Discussion started by: ebsus
3 Replies

4. Shell Programming and Scripting

Match Pattern and print pattern and multiple lines into one line

Hello Experts , require help . See below output: File inputs ------------------------------------------ Server Host = mike id rl images allocated last updated density vimages expiration last read <------- STATUS ------->... (4 Replies)
Discussion started by: tigerhills
4 Replies

5. Shell Programming and Scripting

Removing multiple lines from input file, if multiple lines match a pattern.

GM, I have an issue at work, which requires a simple solution. But, after multiple attempts, I have not been able to hit on the code needed. I am assuming that sed, awk or even perl could do what I need. I have an application that adds extra blank page feeds, for multiple reports, when... (7 Replies)
Discussion started by: jxfish2
7 Replies

6. Shell Programming and Scripting

awk to print lines based on text in field and value in two additional fields

In the awk below I am trying to print the entire line, along with the header row, if $2 is SNV or MNV or INDEL. If that condition is met or is true, and $3 is less than or equal to 0.05, then in $7 the sub pattern :GMAF= is found and the value after the = sign is checked. If that value is less than... (0 Replies)
Discussion started by: cmccabe
0 Replies

7. UNIX for Beginners Questions & Answers

UNIX script to append multiple text files into one file based on pattern present in filaname

Hi All-I am new to Unix , I need to write a script. Can someone help me with a requirement where I have list of files in a directory, I want to Merge the files if a pattern of string matches in filenames? AAAL_555A_ORANGE1_F190404.TXT AAAL_555A_ORANGE2_F190404.TXT AAAL_555A_ORANGE3_F190404.TXT... (6 Replies)
Discussion started by: Shankar455
6 Replies

8. Shell Programming and Scripting

Match text to lines in a file, iterate backwards until text or text substring matches, print to file

hi all, trying this using shell/bash with sed/awk/grep I have two files, one containing one column, the other containing multiple columns (comma delimited). file1.txt abc12345 def12345 ghi54321 ... file2.txt abc1,text1,texta abc,text2,textb def123,text3,textc gh,text4,textd... (6 Replies)
Discussion started by: shogun1970
6 Replies

9. UNIX for Beginners Questions & Answers

Reading a file line by line and print required lines based on pattern

Hi All, i want to write a shell script read below file line by line and want to exclude the lines which contains empty value for MOUNTPOINT field. i am using centos 7 Operating system. want to read below file. # cat /tmp/d5 NAME="/dev/sda" TYPE="disk" SIZE="60G" OWNER="root"... (4 Replies)
Discussion started by: balu1234
4 Replies
regex(1F)                                                          FMLI Commands                                                         regex(1F)

NAME
regex - match patterns against a string SYNOPSIS
regex [-e] [ -v "string"] [ pattern template] ... pattern [template] DESCRIPTION
The regex command takes a string from the standard input, and a list of pattern / template pairs, and runs regex() to compare the string against each pattern until there is a match. When a match occurs, regex writes the corresponding template to the standard output and returns TRUE. The last (or only) pattern does not need a template. If that is the pattern that matches the string, the function simply returns TRUE. If no match is found, regex returns FALSE. The argument pattern is a regular expression of the form described in regex(). In most cases, pattern should be enclosed in single quotes to turn off special meanings of characters. Note that only the final pattern in the list may lack a template. The argument template may contain the strings $m0 through $m9, which will be expanded to the part of pattern enclosed in ( ... )$0 through ( ... )$9 constructs (see examples below). Note that if you use this feature, you must be sure to enclose template in single quotes so that FMLI does not expand $m0 through $m9 at parse time. This feature gives regex much of the power of cut(1), paste(1), and grep(1), and some of the capabilities of sed(1). If there is no template, the default is $m0$m1$m2$m3$m4$m5$m6$m7$m8$m9. OPTIONS
The following options are supported: -e Evaluates the corresponding template and writes the result to the standard output. -v "string" Uses string instead of the standard input to match against patterns. EXAMPLES
Example 1: Cutting letters out of a string To cut the 4th through 8th letters out of a string (this example will output strin and return TRUE): `regex -v "my string is nice" '^.{3}(.{5})$0' '$m0'` Example 2: Validating input in a form In a form, to validate input to field 5 as an integer: valid=`regex -v "$F5" '^[0-9]+$'` Example 3: Translating an environment variable in a form In a form, to translate an environment variable which contains one of the numbers 1, 2, 3, 4, 5 to the letters a, b, c, d, e: value=`regex -v "$VAR1" 1 a 2 b 3 c 4 d 5 e '.*' 'Error'` Note the use of the pattern '.*' to mean "anything else". Example 4: Using backquoted expressions In the example below, all three lines constitute a single backquoted expression. This expression, by itself, could be put in a menu defini- tion file. Since backquoted expressions are expanded as they are parsed, and output from a backquoted expression (the cat command, in this example) becomes part of the definition file being parsed, this expression would read /etc/passwd and make a dynamic menu of all the login ids on the system. `cat /etc/passwd | regex '^([^:]*)$0.*$' ' name=$m0 action=`message "$m0 is a user"`'` DIAGNOSTICS
If none of the patterns match, regex returns FALSE, otherwise TRUE. NOTES
Patterns and templates must often be enclosed in single quotes to turn off the special meanings of characters. Especially if you use the $m0 through $m9 variables in the template, since FMLI will expand the variables (usually to "") before regex even sees them. Single characters in character classes (inside []) must be listed before character ranges, otherwise they will not be recognized. For exam- ple, [a-zA-Z_/] will not find underscores (_) or slashes (/), but [_/a-zA-Z] will. The regular expressions accepted by regcmp differ slightly from other utilities (that is, sed, grep, awk, ed, and so forth). regex with the -e option forces subsequent commands to be ignored. In other words, if a backquoted statement appears as follows: `regex -e ...; command1; command2` command1 and command2 would never be executed. However, dividing the expression into two: `regex -e ...``command1; command2` would yield the desired result. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWcsu | +-----------------------------+-----------------------------+ SEE ALSO
awk(1), cut(1), grep(1), paste(1), sed(1), regcmp(3C), attributes(5) SunOS 5.10 12 Jul 1999 regex(1F)
All times are GMT -4. The time now is 08:18 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy