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Top Forums UNIX for Beginners Questions & Answers Pattern matching using awk from a file Post 303045531 by Sanchari on Monday 30th of March 2020 07:28:41 PM
Old 03-30-2020
Pattern matching using awk from a file

Hello, I have a very large file (DB_file.txt) with coordinate positions, example:


example for the DB_file.txt
Code:
chr1    1000    2000    chr1    10000    11000    3    281    0    0.459585414218248    0    0    0    1218    1    1.88650643678468    0    0    0    0.000000425582664277006    3.87833663319237    0.000000425597761316606    0.201115300038799    0.743522481235195    0.822936566866982
chr1    1000    2000    chr1    11000    12000    4    281    0    0.459585414218248    0    0    0    459    1    0.710924839477969    0    0    0    0.000000355375953311341    1.75327208538672    0.000000192399150742434    0.068194541602096    0.101318817290739    0.81707019750747
chr1    1000    2000    chr1    12000    13000    5    281    0    0.459585414218248    0    0    0    1415    1    2.19163104109222    0    0    0    0.000000310867653966458    3.44281554060217    0.000000377804900731428    0.128881860609444    0.263803805858084    0.81707019750747
chr1    1000    2000    chr1    13000    14000    1    281    0    0.459585414218248    0    0    0    437    1    0.676850010570529    0    0    0    0.000000285200375223444    1.49690344452761    0.000000164265976667856    0.335040184988013    0.776177861586765    0.837324774202159
chr1    1000    2000    chr1    14000    15000    1    281    0    0.459585414218248    0    0    0    530    1    0.820893605497437    0    0    0    0.000000271516726063383    1.60662404023105    0.000000176306406449545    0.322230259464951    0.799436461434159    0.850447555722604
chr1    1000    2000    chr1    16000    17000    1    281    0    0.459585414218248    0    0    0    490    1    0.758939371120272    0    0    0    0.000000253854147173018    1.41695624386548    0.000000155492795574155    0.343542270137564    0.75754917047966    0.828368055880824
 chr1    1000    2000   chr1    18000    19000    2    281    0    0.459585414218248    0    0    0    130    1    0.201351261725787    0    0    0    0.000000231422263301451    0.691389012939271    0.0000000758710869983566    0.119714987783608    0.152817308925748    0.81707019750747

I have a pattern file with the following:


Code:
chr1    1000    2000    chr1    10000    11000
chr1    1000    2000    chr1    11000    12000
chr1    1000    2000    chr1    12000    13000

For a single query, I am using the command:
Code:
awk '{if ($1 == "chr1" && $2 == "1000" && $3 == "2000" && $4 == "chr1" && $5 == "38000" && $6 == "39000") print $0}'  DB_file.txt

How can I do for all the patterns in a file ?
 

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PTARGREP(1)						 Perl Programmers Reference Guide					       PTARGREP(1)

NAME
ptargrep - Apply pattern matching to the contents of files in a tar archive SYNOPSIS
ptargrep [options] <pattern> <tar file> ... Options: --basename|-b ignore directory paths from archive --ignore-case|-i do case-insensitive pattern matching --list-only|-l list matching filenames rather than extracting matches --verbose|-v write debugging message to STDERR --help|-? detailed help message DESCRIPTION
This utility allows you to apply pattern matching to the contents of files contained in a tar archive. You might use this to identify all files in an archive which contain lines matching the specified pattern and either print out the pathnames or extract the files. The pattern will be used as a Perl regular expression (as opposed to a simple grep regex). Multiple tar archive filenames can be specified - they will each be processed in turn. OPTIONS
--basename (alias -b) When matching files are extracted, ignore the directory path from the archive and write to the current directory using the basename of the file from the archive. Beware: if two matching files in the archive have the same basename, the second file extracted will overwrite the first. --ignore-case (alias -i) Make pattern matching case-insensitive. --list-only (alias -l) Print the pathname of each matching file from the archive to STDOUT. Without this option, the default behaviour is to extract each matching file. --verbose (alias -v) Log debugging info to STDERR. --help (alias -?) Display this documentation. COPYRIGHT
Copyright 2010 Grant McLean <grantm@cpan.org> This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2014-09-30 PTARGREP(1)
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