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
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
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
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
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
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
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
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
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
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
LEARN ABOUT XFREE86
regex
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)