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Top Forums UNIX for Dummies Questions & Answers Grep? - using a file of terms to search another file when the information is on a different line Post 302843663 by Twinklefingers on Wednesday 14th of August 2013 10:51:00 AM
Old 08-14-2013
Grep? - using a file of terms to search another file when the information is on a different line

I have a flat file that looks like this, let's call it Chromosome_9.txt:
Code:
FT                   /Gene_Name="Guanyl-Acetylase 9"
FT                   /Gene_Number"36952"
FT                   /Gene_Name="Endoplasmic Luciferase"
FT                   /Gene_Number"36953"
FT                   /Gene_Name="Variant Antigen Protein 12"
FT                   /Gene_Number"36954"
FT                   /Gene_Name="Acyl-CoA Synthetase 11"
FT                   /Gene_Number"36955"
FT                   /Gene_Name="Conserved protein, unknown function"
FT                   /Gene_Number"36956"

This is a file in a specialized format that contains all the information about genes on a chromosome, including the names and associated numbers. What I have is a list of numbers ("/Gene_Number," above), like this, let's call it gene_names.txt:
Code:
2568
3658
9567
23657
63654
76532

but I need the names associated with those numbers (on the line above the number in the file). This would be trivial is they were on the same line because then I could use:
Code:
grep -f gene_names.txt Chromosome_9.txt

Because the search term and the actual information I am looking for are on different lines, I am not sure what to do.

Thanks!
 

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POE::Filter::Grep(3pm)					User Contributed Perl Documentation				    POE::Filter::Grep(3pm)

NAME
POE::Filter::Grep - select or remove items based on simple rules SYNOPSIS
#!perl use POE qw( Wheel::FollowTail Filter::Line Filter::Grep Filter::Stackable ); POE::Session->create( inline_states => { _start => sub { my $parse_input_as_lines = POE::Filter::Line->new(); my $select_sudo_log_lines = POE::Filter::Grep->new( Put => sub { 1 }, Get => sub { my $input = shift; return $input =~ /sudo[d+]/i; }, ); my $filter_stack = POE::Filter::Stackable->new( Filters => [ $parse_input_as_lines, # first on get, last on put $select_sudo_log_lines, # first on put, last on get ] ); $_[HEAP]{tailor} = POE::Wheel::FollowTail->new( Filename => "/var/log/system.log", InputEvent => "got_log_line", Filter => $filter_stack, ); }, got_log_line => sub { print "Log: $_[ARG0] "; } } ); POE::Kernel->run(); exit; DESCRIPTION
POE::Filter::Grep selects or removes items based on simple tests. It may be used to filter input, output, or both. This filter is named and modeled after Perl's built-in grep() function. POE::Filter::Grep is designed to be combined with other filters through POE::Filter::Stackable. In the "SYNOPSIS" example, a filter stack is created to parse logs as lines and remove all entries that don't pertain to a sudo process. (Or if your glass is half full, the stack only selects entries that DO mention sudo.) PUBLIC FILTER METHODS
In addition to the usual POE::Filter methods, POE::Filter::Grep also supports the following. new new() constructs a new POE::Filter::Grep object. It must either be called with a single Code parameter, or both a Put and a Get parameter. The values for Code, Put, and Get are code references that, when invoked, return true to select an item or false to reject it. A Code function will be used for both input and output, while Get and Put functions allow input and output to be filtered in different ways. The item in question will be passed as the function's sole parameter. sub reject_bidoofs { my $pokemon = shift; return 1 if $pokemon ne "bidoof"; return; } my $gotta_catch_nearly_all = POE::Filter::Grep->new( Code => &reject_bidoofs, ); Enforce read-only behavior: my $read_only = POE::Filter::Grep->new( Get => sub { 1 }, Put => sub { 0 }, ); modify modify() changes a POE::Filter::Grep object's behavior at run-time. It accepts the same parameters as new(), and it replaces the existing tests with new ones. # Don't give away our Dialgas. $gotta_catch_nearly_all->modify( Get => sub { 1 }, Put => sub { return shift() ne "dialga" }, ); SEE ALSO
POE::Filter for more information about filters in general. POE::Filter::Stackable for more details on stacking filters. BUGS
None known. AUTHORS &; COPYRIGHTS The Grep filter was contributed by Dieter Pearcey. Documentation is provided by Rocco Caputo. Please see the POE manpage for more information about authors and contributors. perl v5.14.2 2012-05-15 POE::Filter::Grep(3pm)
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