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Top Forums UNIX for Beginners Questions & Answers Grep or awk a unique and specific word across many fields Post 302999191 by daashti on Thursday 15th of June 2017 06:45:47 AM
Old 06-15-2017
it shouldn't as the next filed has hetero. it should look for all fields after the 6th column.

I am trying to create to separate files one with hetero and one with homo. if its easier to code that way.

input:
Code:
CHR	START-SNP	END-SNP	REF	ALT	PATIENT1	PATIENT2	PATIENT3	PATIENT4
chr1	69511	69511	A	G	homo	hetero	homo	hetero
chr2	69513	69513	T	C	.	hetero	homo	hetero
chr3	69814	69814	G	C	.	.	homo	homo
chr4	69815	69815	C	A	hetero	.	.	hetero

when grep/awk for hetero
output 1:
Code:
CHR	START-SNP	END-SNP	REF	ALT	PATIENT1	PATIENT2	PATIENT3	PATIENT4
chr4	69815	69815	C	A	hetero	.	.	hetero

when grep/awk for homo
output 2:
Code:
CHR	START-SNP	END-SNP	REF	ALT	PATIENT1	PATIENT2	PATIENT3	PATIENT4
chr3	69814	69814	G	C	.	.	homo	homo

BTW the file I have has many PATIENT1-10000 columns
 

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Mail::Box::Search::Grep(3pm)				User Contributed Perl Documentation			      Mail::Box::Search::Grep(3pm)

NAME
Mail::Box::Search::Grep - select messages within a mail box like grep does INHERITANCE
Mail::Box::Search::Grep is a Mail::Box::Search is a Mail::Reporter SYNOPSIS
use Mail::Box::Manager; my $mgr = Mail::Box::Manager->new; my $folder = $mgr->open('Inbox'); my $filter = Mail::Box::Search::Grep->new ( label => 'selected' , in => 'BODY', match => qr/abc?d*e/ ); my @msgs = $filter->search($folder); my $filter = Mail::Box::Search::Grep->new ( field => 'To' , match => $my_email ); if($filter->search($message)) {...} DESCRIPTION
Try to find some text strings in the header and footer of messages. Various ways to limit the search to certain header fields, the whole header, only the body, the whole message, but even binary multiparts, are provided for. The name grep is derived from the UNIX tool grep, which means: "Get Regular Expression and Print". Although you can search using regular expressions (the Perl way of them), you do not have to print those as result. METHODS
Constructors Mail::Box::Search::Grep->new(OPTIONS) Create a UNIX-grep like search filter. -Option --Defined in --Default binaries Mail::Box::Search <false> decode Mail::Box::Search <true> delayed Mail::Box::Search <true> deleted Mail::Box::Search <false> deliver undef field undef in Mail::Box::Search <$field ? 'HEAD' : C<'BODY'>> label Mail::Box::Search undef limit Mail::Box::Search 0 log Mail::Reporter 'WARNINGS' logical Mail::Box::Search 'REPLACE' match <required> multiparts Mail::Box::Search <true> trace Mail::Reporter 'WARNINGS' binaries => BOOLEAN decode => BOOLEAN delayed => BOOLEAN deleted => BOOLEAN deliver => undef|CODE|'DELETE'|LABEL|'PRINT'|REF-ARRAY Store the details about where the match was found. The search may take much longer when this feature is enabled. When an ARRAY is specified it will contain a list of references to hashes. Each hash contains the information of one match. A match in a header line will result in a line with fields "message", "part", and "field", where the field is a Mail::Message::Field object. When the match is in the body the hash will contain a "message", "part", "linenr", and "line". In case of a CODE reference, that routine is called for each match. The first argument is this search object and the second a reference to same hash as would be stored in the array. The "PRINT" will call printMatchedHead() or printMatchedBody() when any matching header resp body line was found. The output is minimized by not reprinting the message info on multiple matches in the same message. "DELETE" will flag the message to be deleted in case of a match. When a multipart's part is matched, the whole message will be flagged for deletion. field => undef|STRING|REGEX|CODE Not valid in combination with "in" set to "BODY". The STRING is one full field name (case-insensitive). Use a REGEX to select more than one header line to be scanned. CODE is a routine which is called for each field in the header. The CODE is called with the header as first, and the field as second argument. If the CODE returns true, the message is selected. in => 'HEAD'|'BODY'|'MESSAGE' label => STRING limit => NUMBER log => LEVEL logical => 'REPLACE'|'AND'|'OR'|'NOT'|'AND NOT'|'OR NOT' match => STRING|REGEX|CODE The pattern to be search for can be a REGular EXpression, or a STRING. In both cases, the match succeeds if it is found anywhere within the selected fields. With a CODE reference, that function will be called each field or body-line. When the result is true, the details are delivered. The call formats are $code->($head, $field); # for HEAD searches $code->($body, $linenr, $line); # for BODY searches The $head resp $body are one message's head resp. body object. The $field is a header line which matches. The $line and $linenr tell the matching line in the body. Be warned that when you search in "MESSAGE" the code must accept both formats. multiparts => BOOLEAN trace => LEVEL Searching $obj->inBody(PART, BODY) See "Searching" in Mail::Box::Search $obj->inHead(PART, HEAD) See "Searching" in Mail::Box::Search $obj->search(FOLDER|THREAD|MESSAGE|ARRAY-OF-MESSAGES) See "Searching" in Mail::Box::Search $obj->searchPart(PART) See "Searching" in Mail::Box::Search The Results $obj->printMatch([FILEHANDLE], MATCH) $obj->printMatchedBody(FILEHANDLE, MATCH) $obj->printMatchedHead(FILEHANDLE, MATCH) Error handling $obj->AUTOLOAD() See "Error handling" in Mail::Reporter $obj->addReport(OBJECT) See "Error handling" in Mail::Reporter $obj->defaultTrace([LEVEL]|[LOGLEVEL, TRACELEVEL]|[LEVEL, CALLBACK]) Mail::Box::Search::Grep->defaultTrace([LEVEL]|[LOGLEVEL, TRACELEVEL]|[LEVEL, CALLBACK]) See "Error handling" in Mail::Reporter $obj->errors() See "Error handling" in Mail::Reporter $obj->log([LEVEL [,STRINGS]]) Mail::Box::Search::Grep->log([LEVEL [,STRINGS]]) See "Error handling" in Mail::Reporter $obj->logPriority(LEVEL) Mail::Box::Search::Grep->logPriority(LEVEL) See "Error handling" in Mail::Reporter $obj->logSettings() See "Error handling" in Mail::Reporter $obj->notImplemented() See "Error handling" in Mail::Reporter $obj->report([LEVEL]) See "Error handling" in Mail::Reporter $obj->reportAll([LEVEL]) See "Error handling" in Mail::Reporter $obj->trace([LEVEL]) See "Error handling" in Mail::Reporter $obj->warnings() See "Error handling" in Mail::Reporter Cleanup $obj->DESTROY() See "Cleanup" in Mail::Reporter $obj->inGlobalDestruction() See "Cleanup" in Mail::Reporter DIAGNOSTICS
Error: Package $package does not implement $method. Fatal error: the specific package (or one of its superclasses) does not implement this method where it should. This message means that some other related classes do implement this method however the class at hand does not. Probably you should investigate this and probably inform the author of the package. SEE ALSO
This module is part of Mail-Box distribution version 2.105, built on May 07, 2012. Website: http://perl.overmeer.net/mailbox/ LICENSE
Copyrights 2001-2012 by [Mark Overmeer]. For other contributors see ChangeLog. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See http://www.perl.com/perl/misc/Artistic.html perl v5.14.2 2012-05-07 Mail::Box::Search::Grep(3pm)
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